Steffen

You shouldn't be put off by the problems we are experiencing. If your players are cooperative and you didn't have problems with them before you will probably also not have problems with them when playing Champions.

Thanks for the good wishes but as I wrote when resurrecting the thread we will only play about two more times to finish the story arc and then never again play Champions with the non-compliant players. The complaints and discussions have spoiled the  campaign for my girlfriend (Magical Girl character) and me.

Yes, we started our first session with 100 point characters but everyone was fully aware that the characters would only be slightly super in the beginning. The GM told us that we could only afford 2-4 powers for the first session but that we would be able to increase or buy powers very quickly although it would take some time before we would be as powerful as comic book or movie superheroes. Our characters should start as "people with powers" similar to the "Heroes" TV show so that criminals with guns would pose a danger and slowly evolve into superheroes.
During the first session we played the origin story, discovered and used some of our new powers and mainly talked and used skills. We got 10 points for this and 5-15 points after the following sessions so we could quickly improve our characters.
 
Maybe there is a communication problem but then it is with the two other players who dismiss the information they receive from the GM.

That's correct. The GM tried to keep the challenges and fights suitable for our characters.
 
However, I have to admit that the low starting points have been a problem for the player of the TK character. She wanted to make a reluctant character that would would never be seen with the group and would look like an innocent bystander when using her powers while the rest of us were fighting villains. All of her powers were supposed to be completely invisible and cost no endurance at all but this resulted in a very low TK Strength and Blast so she was unhappy. Oh yes, and she wanted to have a gun.
 
The GM was unhappy because from the start he had asked us to create good superheroes without Killing Attacks that wanted to help people and explicitly mentioned to not have brooding misanthropes with deep seated emotional problems that refused to be part of the group.
 
The ensuing discussions and arguments were the main reason why my enthusiasm was quickly curbed.

The original question was not how the character concept could be built, it was if the concept should be allowed. The GM was aware that a VPP was the most logical way to build it but decided that he didn't want VPPs in his campaign for (legitimate) fear of abuse.
 
The GM simply didn't want a superhero with the theme "all the powers the player thinks are useful".

I think you are absolutely right although I do not blame Champions or the HERO system at all. I only think that it is not suitable for everyone. Or maybe not everyone is suitable for the HERO system.
 
Although he knows the approach of the players to roleplaying for more than two decades the GM underestimated the problems that would arise. I think he simply trusted that everyone understood what he wanted but didn't expect that he had to supervise everything.
 
I'm also quite sure that the other two players really believe that they are being treated unfair because they are not allowed to have the characters they want and should be able to build using the HERO system. The rules clearly state that the system can build everything but it is the GM who keeps them from doing so.

Example scenario (blatantly stealing an idea from a Warehouse 13 episode):
 
The PCs are attending the local museum's unveiling of their Ancient Cultures exhibit, featuring items from ancient Egypt, Assyria, Babylonia, and Sumeria.  This corresponds with an annual fundraising dinner, so a lot of the city's movers and shakers are there as well.  Caterers, guards, visitors, reporters, students, the well-to-do: a wide selection of people are there.
 
After a bit of the PCs wandering around and the GM describing the various items on display, including a stone statue of Sumerian god Anunnaki and the sarcophagus of the Egyptian 13th Dynasty pharaoh Amehemhet VI, and an odd semi-circular stone that feels like it's vibrating slightly (and visitors are encouraged to touch if they wish).  A section of stone wall, inscribed with hieroglyphs and paintings of Horus and Osirus, separates the Egyptian exhibit from the Sumerian.  The PCs hear Dr. Richard Reynolds, the museum's curator, arguing with an archaeology grad student about the translation on a stone tablet or the stone wall, with the grad student, emphasizing his words by repeatedly poking the tablet / wall with his index finger, when a bright light temporarily blinds everybody, and a wave of energy is released from the stone tablet / wall (giving the PCs their powers, as well as various NPCs).  When everybody can see again, they notice a number of museum visitors / staff / VIPS are gone, replaced with shadowy figures who begin attacking the bystanders and PCs.  (Cue intro fight, with the PCs somehow knowing what types of powers they now have thanks to the spirits that empowered them.)  Any shadowy figures not captured will retreat but not leave the premises.  (Actually, nobody can leave due to a strange energy dome that is now encompassing the museum, erected by the beneficial spirits / deities to help the PCs.)  Their ability to pass through walls should be a pain for the heroes, as well as their ability to temporarily possess innocent bystanders.
 
The PCs eventually learn that the missing people weren't transformed into the shadowy figures (which they might initially suspect), but are instead trapped in the obsidian mirror while the shadow figures were apparently freed from the mirror, which the PCs' research uncovers was actually the shadow figures' prison for millennia.  Also, they PCs learn from their benevolent spirits that when dawn comes, the energy dome will end and the shadowy figures can go anywhere they wish. 
 
The PCs then have to figure out how to re-trap the shadow figures inside the mirror, which will release the innocent people trapped there.  This likely requires capturing all of the shadow figures and bringing them into the room with the obsidian mirror, then performing a ritual of some sort. 
 
That's my rough outline.  Feel free to change / add / ignore whatever you wish.

1.  Make sure the players are all on the same page as you regarding a shared origin revealed in-game.  Everybody may be cool with the idea, but it still wouldn't hurt to talk to them beforehand and ensure they're all okay with the idea.
 
2.  I'm assuming the spirits inhabiting / empowering the PCs are benevolent spirits / deities, and those empowering the bad guys are natively bad themselves.  I'd suggest those benevolent spirits might provide their PCs with info on select bad guys' spirits / powers.  For example the Horus-empowered PC might have key info on the Set-empowered NPC villain, while the plant-powered PC has info on a different villain, etc.  This can maybe lay the groundwork for some arch-nemeses in an ongoing campaign.
 
2a.  The link between the empowering spirits and the PCs might also provide some odd skills that the PCs might not have naturally.  For example, the Horus PC may inexplicably now be able to read hieroglyphs, the animal PC now has a great Tracking skill without knowing anything about tracking prior to the event.  Having a secret set of skills (nothing major, say 5 points worth) that the players learn about in-game could be cool for the players, and if selected and presented well could provide opportunities to spotlight different PCs throughout the scenario.  ("As the museum curator is stumbling through translating the Sumerian text, you realize you intimately know about the ancient artifact he's describing, including how to activate it.  It's like someone is whispering the info in your mind.")
 
3.  Regarding the museum event, this could be a fundraiser or the opening of a new exhibit (or both combined).  Regardless, I'd make sure you include non-powered bystanders, in addition to those gaining powers from the evil spirits.  Perhaps the darkness spirits trap a handful of bystanders (including a DNPC or two for the PC heroes?) in an extra-dimensional shadow realm, and the heroes have to figure out where they disappeared to, and then a way to free them before dawn.  Thus, the non-combat investigation and research.  Whether the PCs have to travel to the shadow realm themselves, or just open the door to allow the hostages to be freed, is up to you.
 
For example, a large slab of volcanic obsidian, polished to a mirror finish, with Sumerian cuneiforms inscribed around the periphery, is part of the new exhibit, but is not part of the whole empowering thing.  It's only after people disappeared and the search is on that one of the PCs notices there's more "reflections" in the mirror than there are people in the room with him.
 
4.  Flesh out a few non-powered NPCs (a reporter, a professor from the nearby university, an unappreciated underling at the museum, a beat cop moonlighting as a museum security guard, etc.)  that are key to the plot.  You don't need full writeups, but a paragraph or two and a handful of key stats / skills on each to make them a little more three-dimensional. 
 
That's just a few ideas off the top of my head.