Alcibiades

Yeah some limited shapeshift and stretching, and damage reduction seems to serve well to represent something made up of a lot of creatures.  Also, consider cannot be stunned and does not bleed automaton powers to represent that you really will have a hard time stunning all of them (or even a large number).

You can simplify this a bit by asking the question "do I want a specific mechanic related to this?"
 
Remember that you _can_ have a mechanic-- an "in-game effect"-- attached to anything you want.  But you are _never_ required to have one attached to _anything_.  If you just want something to "be this way" but have no actual gain from it, then you declare it as a special effect but don't assign a mechanic to it.  For example, let's say you are making a PC with heterochromia (his eyes are two different colors).  It's different from any PC you've made before (maybe), but you don't have to buy any special mechanic to do it.  You don't even have to buy a disadvantage to represent it.
 
[this break conveniently left to make quoting and arguing this point easier]
 
 
 
 
 
 
 
 
Here's the thing with the heterochromia example:
 
You _can_ do it.  You _can_ declare that this is Unstinctive Fealooks or whatever Disadplication you want, and suffer all the negatives associated with it.  Even then, you don't have to.  Heterochromia isn't exactly common, but you have most likely met someone who has it, or seen a cat with it (not sure why: it's more common in cats than in people, but not by much).  I have met three people with it.  Given the number of people I have met in sixty years-- well, it's not common.     Just as an example, I remember _two_ of those people by name, and I could only give you a really accurate description of the girl I dated who had it.  The other one I could name I can describe as "light-skinned African American, Jehova's Witness (because he made a big deal out of it), I had a microbiology class with him." I can tell you his first name (because it was the same name as one of my uncles, otherwise I probably couldn't do that)  i couldn't even tell you what colors his eyes actually _were_.  In fact, the only reason I know I've met three is because when I met the Jehova's Witness, I recall thinking "Wow!  Now I've seen _two_ people with heterochromia!  Neat!"  I might have been able to describe the first back then; I don't remember.  I doubt it.  I certainly can't do it now.
 
Given that when we talk to someone, we tend to look into _one_ eye when we look "in their eyes," I may have met more than three without actually realizing it.
 
Anyway, you can take a Disad for it or not.  If you don't have "complications" from it, then don't.  Just because you can conceive of something being a problem does _not_ mean that it is a problem, always, for everyone, forever and ever, period.  it just doesn't.
 
It's the same thing with positives, too.
 
So your swarm can change sizes and shapes.
 
You have to decide if doing so gives the swarm any positives-- any unique in-game effects that must be purchased.  Perhaps it's stretching, allowing them to grab, move, or attack things way far away.  Perhaps they can't actually do that for whatever reason strikes your fancy-- when stretched too thin, there are not enough of them to exert any strength, maybe.  Maybe it's a Flash Attack-- the droning and buzzing makes it difficult to hear or see.  Or maybe they can't do that, either, when stretched too thin.
 
Perhaps it's a couple of dice of Presence Attack-- like when a goose spreads its wings or an elephant straightens its ears: it's meant to make the swarm look larger and more dangerous.
 
Maybe it's not even that.
 
Maybe there is absolutely no mechanical effect at all; the swarm just _does_ that-- like the murmuration of starlings.  
 
If that's the case, it's just Special Effects of being that particular swarm, and you don't have to pay for it.
 
 
 

I believe you are overthinking this.  You're adding in an Advantage where there doesn't need to be one.
 
Invisibility
Zero End (+1/2), Persistent (+1/4)
11- Activation roll (-1)
Limited Power: roll for each target individually each phase (-0)
 
Done.  The limited power is a -0 because it's not particularly advantageous, nor really extra limiting.  A basic 11- would mean that some phases, nobody can see you, while other times everyone can see you.  Rolling individually means that it'll never be as good as when you're invisible to everyone, but it'll never be as bad as when you're invisible to no one.

Oh man, I wish Lovecraft had written about giant albino penguins!

The Ark was also supposed to be a divine weapon of antiquity. I'm not familiar with any works by Lovecraft in which an Elder God was carried around in a vessel and used by kings and generals to lay waste to armies on the battlefield. Moreover, I don't believe that the final scene with the Ark was intended to be interpreted as the unleashing of a Nameless Cosmic Horror From Beyond. If anything it was the Vengeance of Yaweh unleashed upon evil Men (the virtuous "heroes" at the scene, like Indy and Marian, were simply collateral damage).
 
But more important than any of that, the tone of the Indiana Jones series is utterly non-Lovecraftian.

He would also have Lovecraft as a contact!

He would also have Lovecraft as a contact!