[quote name='zohar']Anyone know the difference between the 3DS and Wii-U versions?[/QUOTE]
The WiiU version has some Nintendo nouns from the Mario and Zelda franchises, but you can't apply adjetives to them and they do nothing whatsoever but walk around (and Peach/Zelda may run away from Ganon/Bowser), so the novelty wears off very quickly. It has a girlfriend mode where anyone with a wiimote can control any non-Nintendo related item you create, but again, this really adds nothing.
The only addition really worth mentioning is the item creation tool. I haven't worked with it myself yet but I've downloaded some things from other people, it's actually kinda neat. Certainly not enough to justify the outragous price for Scribblenauts U, and certainly not enough to justify paying $40 for it on WiiU vs $20 or so on PC/3DS, but it's not a useless feature either. I'm pretty impressed with a lot of the Pokemon people have uploaded, if you have the patience to find it on the UGC "shop".
That's about it. I'd stick with the 3DS version at $20, you aren't really missing on any worthwhile content/story/graphics/ect. In fact, even the WiiU version feels very much like a portable title, even in TV mode the entire game is constantly displayed on the Gamepad, the only real difference is whether you want to listen to the music/sound through the Gamepad or the TV.