I think a lot of balancing can be achieved simply by moving some gear abilities into being regular abilities.
For instance, give Supergirl her sunstone armour as a regular ability. For those unfamiliar with that, it reduces the damage she takes, but she can't use her eye lasers while its active. It makes for an interesting play style with her and let's her mix up how she plays. Give Robin the Staff of Greyson as his character trait instead of that useless thing you always forget about and need to work really hard to find a way to make even marginally useful. Give Poison Ivy her slide, Green Lantern his machine gun and Captain Cold his ice platforms.
A lot of characters are just missing one thing to make them competitive against the higher tier characters and, in many cases, that thing has already been put into the game. Make it part of their main move set and they're good to go.
For other changes, make Grodd's trait moves full screen instead of just giving him a couple more moves which work about the same as his regular moves. Also, make his projectile immunity thing DB1 instead of DD1, so it's not so awkward to try and input when someone's shooting at you. Also, give him new dialogue - the whole "Kneel before Grodd" thing was funny for about a week, but now it's gotten old.
For WW, don't have all of her special moves knock the opponent full screen, so she needs to start from scratch to get in on them again. Even if you just have the meter burn versions drop them close, it would give her the option to have them end up there. I'm also probably one of the only people who likes her random trait - it makes her more unique to play.
Give Swamp Thing something that would give me a reason to play him and be able to even make a comment about the character.
In terms of nerfs, I'd increase the recovery time on Batman's batarangs, so he can't fire them off as quickly. He's awesome up close, he doesn't need to be an awesome zoner as well - he can just be ok. Have Superman's laser be a low and stay a low and not just track up to hit jumping guys unless it's meter burned. Take away Deadshot's knock back bullets (the blue ones) so they don't completely undo people trying to get in on him. Give Catwoman's B3 less of a low profile so she can't just fire it off underneath half the casts' punches.
This is scrappy a fairly well balanced game so balance changes don't need to be huge for the most part to make everyone more on the same level.
