I can see a few issues with this... but honestly....nothing that couldn't be overcome. You might be better off having limited units of actual Superhero's with small numbers of powerful soldiers ( like elephant units...not many but lethal! ) and make up the bulk of the cannon fodder as 'avatar' soldiers. Dressed in the correct colours, but not actually superhero powerful.

That way, you could have a small unit of Cyclops fire-beaming a load of peasants carrying Captain America shields and banners. Gives you far more opportunity to see units being blasted about by very powerful warriors, and makes it a little easier to cope with the quantity of Superhero's.

Just a thought ... and it reduces the amount of model variations you are going to need to really flesh out the thing.