Pros

• Generally really fun. Game makes you feel powerful
• Gfx are waaaaay smoother and look better than MUA1, which was far too "glossy" and stiff looking in combat
• Little comments and wise-cracks during combat are hilarious
• Love the fully destructible environments.  Almost everything falls apart or blows up. Makes you feel super :D
• Way more enemies on screen at once, and they have pretty low hp... makes you feel strong when you rip them to shreds
• Great story helps drive the game.  Writing is excellent too and has lots of humor.
• Fusion powers are relevant and destructive.
• Lots of achievements and unlockables.
• Split story line makes replaying worthwhile. 
• Deadpool

• Invisible walls galore!  The great thing about the other games in this series is that you can explore everything.  If it's explorable, there's probably some hidden treasure.  If its not explorable, there's a giant visible wall stopping you.  But in MUA 2 the maps suddenly 'end' and this discourages you from exploring.  Lame.
• Cut scenes (both pre renders and close-ups of the models) look ass 
• Characters seem smaller on screen than MUA
• No per-hero equipable items, only team-wide boosts.  I was annoyed when they scaled it down in MUA1 from Legends but now items are completely gone :( 
• Maps are small.  There dungeons were huge in Legends and still pretty big and outlandish in MUA1.  Now some sections take 15 mins to run through and you're left wondering "that's it??".  I was surprised several times to suddenly run into the section boss.
• Still cannot modify your character's individual stats (though you were able to in x-men legends .. yet another regression)
• Even with gamma settings, maps are sometimes too dark