I picked up UMvC3 at midnight and played around for a few hours because I'm an idiot. I'm sleepy now.
There are subtle changes to all the mechanics. The way the characters fall when hit are all tweaked just slightly, so it's difficult to pin down exactly what feels so different. It just becomes obvious when you miss a combo that you NEVER miss in Vanilla just because of timing differences.
To me, the new health bars take some getting used to. Not so much the positioning, but the size of them. The wider bars make me think I have more health than I actually do. Stupid, I know, but I found myself losing characters just because I didn't DHC since I thought I had plenty of health.
The meter change is significant. It's very very noticeable in normal play, which means you have to be much more careful with how you spend meter.
They nerfed Morrigan X-Factor. Whyyyyyy? She's such a mixed bag right now. Wesker's still really good, obviously. Dante does ass damage now and builds no meter.

Like, he seriously does a good 100,000 to 200,000 less damage on his bnb combos, and they whiff on many characters like Rocket Raccoon. They seriously hurt him a lot. His double inputs make him much easier to use, though. I don't like the tradeoff.
I messed around with Phoenix Wright a little before I hit the sack. Gathering evidence is going to be kind of tricky on a pad...
Oh, and they added an X-Factor button (L+M+H+S) which is great for pad users, but I won't be able to use it if I want to use Phoenix Wright on pad and access to one-button-dash.