Couple things I would like to see different:
1. More powers- In XML each character has like 16 different powers to choose from. Marvel; UA only had like 8 per character. One thing I would LOVE to see is a change in the appearance of the power attack each time you upgrade it. For example; Thor's lightnting should start off small, and as you level up it should get bigger and "nastier" each time.
2. Better Villians/bosses- Although a few bosses were awesome i.e Ymir, Mephisto, Galactus, many of the villians in this story line had nothing to do with anything going on in the story, i.e Video man (or carnival guy), Scorpion and many others. Throw in some better top tier guys and your good.
3. Different Heroes- I liked the line-up, but it eventually has to change or people will get bored.
4. More costumes like XML: 2.
5. Make characters like Thor, Surfer, and IM be able to lift heavier things.