Wait, I thought the Wii U version wasn't going to have an adventure mode? (Granted I heard about this in July, see:
http://kotaku.com/the-next-super-smash-bros-wont-have-a-story-mode-or-c-906856304) However I do agree with you, Sakurai surely doesn't have a problem pushing back release dates as we all saw with Brawl haha. The one major difference I'm wondering about will be how will the 3DS make up for the screen size on a standard TV? I don't mean HD--whatever to that, really-- but let's think about some of the more elaborate stages we've seen in Smash history, like New prok City or the Temple stage from Melee. While neither of these are used in competitve play, they're still fun for casuals. I'm also concerned how the 3DS will be able to keep all four characters on the same screen without sacrificing visual quality. I'm not saying that the final product will be a mess or anything, but I am interested in how they plan to overcome these hurdles.
I would say that game modes would definitely be based on the system, and the stages reflect this. I can see the Wii U version being a bit more expansive than the 3DS in some areas, but I think the as a whole the games will take on a "similar but different" tone from one another.