Which is better at 500 pts in a game where per turn each character can destroy one wall or square of blocking terrain as a free action.

SM Black Adam 300
Full Gauntlet
3X Scarlet Witch
Mighty Avengers ATA X2

Worldbreaker 350
Full Gauntlet
2X Scarlet Witch
Mighty Avengers ATA X2

Which will have a higher chance of winning?

I would go with Black Adam and 3 perplex. It also means that your opponent is going to get a minimum of 3 clix of damage going against the 3 Mystical SW.

Anyone can go ahead and correct me if I got this wrong but I don't think you can assign ATA to only a partial number of team members. For the Black Adam team, you have 3 Avengers and if you want to use that ATA for Avengers, you need to assign it to all 3 Scarlet Witches. Since you are lacking in points, it would be advisable that you use the Monster Society of Evil ATA on Black Adam instead. Or Black Adam, JL52 Enchantress, SW x2, Mighty (or Secret) Avengers ATA x2.

You're correct. When using an ATA you have to assign it to all eligible figures on your team. So the Adam team would be 2 points over.