@Master Bruce
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1. Could a player start with a character on an alternate Earth?
Like if someone wanted to play as Val-Zod from New 52 Earth 2, the Joker from the Tangent Universe or Spider-Gwen.
Or would that be too... complicated?
2. What if one player wanted to play Kal-El and another wanted to play Val-Zod? Could both characters possibly be accepted and exist in the same world? Or would the GM decide who had the better CS?
3. Would a villain whom started out as a hero (such as Sinestro who was a Green Lantern) be allowed as a main PC?
1 and 2. Theoretically, yes. I'd largely base that off of who is the first to submit an application with the name "Superman" attached to it, and what their opinion of this is, but you could start off from an alternate universe and find your way to the game's. However, I'd suggest waiting to see who plays Superman if you want to co-exist with them, since he's a major PC and that falls under the jurisdiction of his universe.
3. That's alright, as long as they aren't a villain at the time you're playing them. I just don't want antagonists out there that complicate a main hero's mythology with conflicting variations. But in the case of Sinestro specifically, if you wanted to make him the main hero Green Lantern, that's cool with me.