Obviously, saves would be a big one for Mass Effect (though that wasn't big enough to stop me from play ME2 and ME3 on PS3).
But for starters. Most of the multi-platform games (ME3, Arkham City) are coming out about a year too late. Lots of these games have multiplayer, and my friends list on PS3 features many of my real life friends, plus you dudes, and I don't see everyone switching to Wii U right away (not to mention: Friend Codes). Even though I believe the Wii U will be slightly more powerful than 360/PS3 I don't think we'll see games looking any better on it for awhile, this will be early in it's development cycle, and games always tend to look pretty crappy. But most importantly, and I know this doesn't matter for some people, Nintendo has said there still won't be an achievement system. I have a real hard time sitting through a game and not getting anything to show for it, unless there was no other option and it's a game I really want to play (Mario/Zelda/Metroid). When PS3/Steam/360 all have achievement systems, Nintendo's refusal to implement one of their own, just reeks of their usual attempts at trying to be "different".