Mr. R

A classic use of this group comes from an Organization group called The Blood and Dr. McQuark.
 
In it the PCs run into TI as they are stealing some device from some research comp.
 
WHY?
 
To use it to find and loot a crashed, ancient spacecraft full of potentially valuable tech.  Though TI were tangental to the plot really, you could make them central.  Agents of TI are found setting up safe houses in the city.  As players clash with the agents, PM and his supers come in during the actual robbery to keep the players from intervening with the theft.  Now to track down the device and stop what ever plans TI have.  Season appropriately, serve to the PCs.  

Following Mr. R's example, you could slot them in nearly anywhere you could use VIPER. They would be a bit more likely to lead with their supers, but that would be the only real difference.
 
You could probably modify the old Deathstroke module too.
 

A classic use of this group comes from an Organization group called The Blood and Dr. McQuark.
 
In it the PCs run into TI as they are stealing some device from some research comp.
 
WHY?
 
To use it to find and loot a crashed, ancient spacecraft full of potentially valuable tech.  Though TI were tangental to the plot really, you could make them central.  Agents of TI are found setting up safe houses in the city.  As players clash with the agents, PM and his supers come in during the actual robbery to keep the players from intervening with the theft.  Now to track down the device and stop what ever plans TI have.  Season appropriately, serve to the PCs.  

Thank you!

Personally, I prefer multiple magic systems in a Hero Fantasy setting because I feel it offers additional opportunities for character differentiation and highlights one of the Hero System's strongest features.
 
In general it can be difficult to balance different means of empowerment against one another in a given context such as a setting, particularly if those means of empowerment are implemented as orthogonal sub-systems of arbitrary rules. The Hero System and similar game systems influenced by it (or independently evolved) that have a strong notion of separation between fluff and mechanic and a common unified effects model provide a lot of lift to overcome that difficulty. 
 
And so on...I don't have time to wax loquacious on generalities, so I'll forbear further abstraction for now and move on to specifics.
 
The various Fantasy Hero magic systems I offer are meant to be used either together or separately. Some are better for particular power levels or tones, some are more suited to be used as general systems while others are more niche, and some are more by-the-book while others introduce custom mechanics or some structured hand-wavium. However, they are all basically compatible. 
 
As an exercise in dogfooding, back in the days when I was building the bulk of those systems, I made the custom setting of San'Dora with a meta goal of including every single one of those magic systems in one setting. I taped together a bunch of blank paper to make a blank map and drew in a centralized Mediterranean like coastline then passed the otherwise blank canvas around the table of my players at the time and they each extended the map's coastlines, delineated continents, added mountain ranges, forests, rivers, and further geographical embellishments. I then had them each make a list of their favorite genre sources and concepts (books, movies, comics, whatever) and each list 3 things they wanted incorporated into the setting, etc. Then I synthesized all of that into various ages and peoples to incorporate all of it and assigned various magic systems to different cultures, influencing the nature of those cultures and their histories based upon the qualia and power level of their native magic systems. And so on and so forth. This fed back into the magic design, inspiring many of the variants and specializations within the broader systems.
 
Thus, the various magics systems and their relative power levels, tone, etc, actively influenced that particular setting and vice versa, which results in a grounded / organic feel, reinforces cultural notions within the setting, suggests / drives historical detail, and generally acts as an important part of the worldbuilding process.
 
I would recommend a similar approach be taken to ground your chosen magic system(s) and other means to empowerment such as religious and knightly orders, martial styles, significant professions, and so on directly into your setting. And to be clear, not just the superficial "now" of your setting, but from the bottom up starting at the foundation of the setting's conceptual core, layering thru the history / back story thereof unto the present / current era where play will begin. Having taken this approach, a rich tapestry of character origins with verisimilitude and internal consistency will present itself from the resting state of your worldbuilding rather than being no more than a bullet list of tacked on, bolted together choices lacking resonance or contextual relevance.
 
And finally to get maximally specific: my Metier, Runecrafting, and Totemic Shamanism systems all work together reasonably well and I would not expect you to encounter any special problems if you allowed all three. The one caveat there is, as mentioned somewhere in the Runecrafting documentation, as a magic system that revolves around making magic items, you should first work out how you plan to handle magic items in your setting before deciding to incorporate Runecrafting as the assumptions I made when designing that system are based upon how I handled magic items (also documented on the site) which may differ from your assumptions / preferences. 

About five acres of good farmland will support one person, so for a 10,000 person city (like early medieval London) you would need at least 78 square miles of farmland. Assuming less good farmland and twice the population, you would need at least 300 square miles.

A) Too many for what? A setting with only one kind of magic can be focused and challenge players to use what magic is available, exploring it in depth. A world with multiple forms of magic can feel mysterious and open (as the real world was for people in premodern times -- anything could exist just over the horizon), and gives players more options. Though, yes, a large number of magics can also feel arbitrary and encourage an attitude of picking whatever collection of magics seem useful without regard for internal logic.
 
Three sorts of magic that operate in quite different ways, for quite different ends, does not automatically seem excessive to me. But it depends on what sort of setting you intend to create -- and no one else can answer that question for you.
 
That is up to you. If you don't design anything cool for other sorts of characters, then yes, the setting may seem front-loaded on magic.
 
Non-spellcasters can have "non-power Powers" that represent special weapon techniques or other extraordinary training. See Ultimate Martial Artist or Dark Champions for examples.
 
C) That actually does sound liike a good idea. It helps to preserve the mystique of each form of magic so they seem, well, magical, instead of a buffet of arbitrary Powers. Come up with whatever in-setting justification you want.
 
(Unless the whole point of your saga is that some PC is going to become the first multi-caster, as in Hardy's Master of Five Magics. But that's a whole 'nother issue -- and again, is something you must decide for yourself.)
 
Dean Shomshak

My players are powerful at this point, but their teamwork tends to be off and on. The Ultimates use teamwork to make up for their relative lack of offensive punch. The contrast works.

In M&M's Atlas of the World, he was actually a Rakshasa from India working to foil his people's plans for moving outside of India!

I could see Alfred Nobel instead of setting up a system of prizes in penance for inventing dynamite instead funding mystery men to fight evil wherever it is found. And regardless of governments and their laws.
 
He was effectively a multi-millionaire businessman (in today's dollars) who outright owned multiple businesses (including dozens of munitions factories) and had 355 patents for various inventions.

The Star Crown Empire and the Sea of Fates.  It is an old ICE Shadow World module.  
 

The Star Crown Empire and the Sea of Fates.  It is an old ICE Shadow World module.  
 

I agree.  Of the four, these two resonated most with me.  And IF I had to pick one, I'd go with the "Wrongfully Convicted:  Divinely Conscripted"
 
The only problem with that one is if a player leaves or dies, how do you get the next member into the team and still follow the same origin idea?
 
At least "The Price of Dreams" has an out for player/PC turn over!

Oil of De-Squeaking

Oil of De-Squeaking - You apply this oil on some mechanical device which is squeaking and it stops squeaking. It's particularly popular to apply this item to door hinges and to wheels.

flight
gassess form
speed
 

Something like this.  I don't want magical weapons to be those things where "there's the magic item store, where's our list again?" attitude.  I want some normal weapons that are so good as to be considered almost semi magical.  To me that will make those magical weapons/ items something special!

So what is your reason for making steel 'magical'?  Is it just for flavor or does it have an actual effect on the game mechanics? 
 
In my own games, good steel weapons are readily available and follow the standard weapon stats.  But they can also become dull if not maintained, or break if abused (or sometimes on a roll of 18 or when Unluck triggers).  Non-magical weapons made of mithril require much less maintenance and have a lower STR Min than a similar steel weapon.  They are rare and expensive of course.  Even more rare are adamantium weapons which are so exceedingly hard that they can hold an ultra-fine edge that makes the weapon effectively armor-piercing (they have normal STR Min though).  Mithril and adamantium weapons allow for a nice step between standard weapons and fully magical ones as far a loot for the PC's goes.
 
You might also want to consider how the availability of steel will affect armor choices.  Iron armor is going to have -1 PD/ED relative to steel armor for the same weight and so may be less desirable, which might shift people toward lighter armors with a lower defense.  It might also make more exotic armors more viable (e.g. horn armor would be -2 PD/ED relative to steel, but only be 70% of the weight).

That might also explain the giants' motivations (since, as @archer mentioned, they don't need human stuff in general, like orcs do). If the humans occupy the lands that the giants once held, then that means the ancient and sacred places of power for the giants, which might hold the keys to a return to dominance, are in human possession. Perhaps the giants have a leader who seeks to return them to prominence by retaking those places and reclaiming their lost secrets...

Well I have an Empire.  I have a partially explored mountain range to the north and south.  Large forests east and west.  Past the northern mountains are a desert and after that a grassland.  Also a Jungle area to the north west and a LONG mountain chain running north south.  
 
Now I am running no elves or dwarves, just humans, but occasionally you want an opponent that the players can bash on.  Usually this is .... orcs.  But I want to get away from that.  So I thought what other enemies come from mythology that I can use, and I came up with one.  Used by Norse and Celtic stories.  Giants!
 
Even if I make the just 2x bigger than humans they'll have a lot of advantages over regular humans.
 
Now just the need to find places to put them so they can be a recurring threat to the humans of the Central Basin.
 
So how does this sound?
 
I like it better than the dumb orc stereotype, and I am thinking of taking the Firbolg from Tuala Morn and just plopping them in.  

Giants were opponents of the Gods in both Norse and Greek (the Titanomachy) mythologies, so those are places to look for inspiration.
 
In one setting I used, giants were an "elder race," slowly vanishing from the world, leaving behind ruins and cryptic monuments, and represented in the present by isolated individuals wielding strange powers that might be magic or technology, holding onto ancient fears, grudges, ambitions, or just habits, with tired monomaniacal zeal.

There is a VERY large inland sea (like all the Great Lakes Combined but larger) as well as Island Kingdoms to the west of the continent and another to the southeast!

By itself dispel actually works well.  The real problem is that to be of any real use it needs the + ½ advantage to be able to function the way it should in a Fantasy Hero game.   The base dispel will be able to overcome 1.16666… point per point spent.  That works out to a 45 point dispel will on the average take down a 52 point power.  When the + ½ advantage is factored in it drops down to .77777… points per point spent.   So you end up needing to spend 1.3 points per point you want to dispel. 
 
One solution would be to require all spells to take a mandatory – ¼ limitations spell.  Basically you are applying the Unified Power Limitation to spells.  That would allow a character to buy dispel spell and be able to affect any spell with the limitation.  That would mean if a character wants to overcome something besides spells he would either need to purchase a separate dispel or apply the + ½ advantage to his dispel. 

At risk of tooting my own horn, I recommend my "Worldbuilding: Social Design and Social Forces" thread, which I just bumped back up to the top of the page. You might find it useful for fleshing out the "deep structure" of how your setting functions.
 
If you want every city to have something colorful and distinctive (and I wouldn't say that's necessary for *every* city; concentrate your efforts on the places you intend the adventures to happen in), I'll repeat my usual recommendation of Italo Calvino's Invisible Cities. It's quite a short...  prose poem? At any rate, Fantasy from an author who won the Nobel Prize for literature.
 
Dean Shomshak

As humorous as this is... when I was a kid I read a book about the Japanese internment in the USA during WWII. At one point, the main character notices an older Asian man doing gardening. He is perplexed, but he finds out from another boy that the man in Chinese. They then have a discussion about how to tell Japanese people from Chinese people.
 
And you have the same people who will salute a vet when he's wearing his uniform on Veteran's Day and then turn around and then not support Social Security, the VA, and the other things this person needs to survive. Because they don't think of the veteran and the person with a disability as being the same person.
 
So it's not hard for me to believe some people in the MCU hate mutants and not mutates, or they hate mutants and mutates but not science experiments, or they don't have a clear understanding of the difference between them, or any number of other configurations of attitude.