Yeah, I don't like Smash Tour myself. While I didn't find it confusing, it was tedious at best.
The Wii U version may be an overall better game than the 3DS version, but the latter had a better mode in Smash Tour's place, Smash Run. Sure, that one had a ton of enemies spawn and hit you more frequently than not, but I thought it was fun, warts and all. Maybe it's to do with the fact that it's the closest thing to an Adventure Mode in either version. Smash Tour is just boring.
I'd even go as far as to use that hammer when a space in the challenges said "Smash Tour" on them simply because I really don't want to go back to that mode!
That said, I'll state the things I like about the Wii U version. The graphics are improved, obviously, and there is a bit more variety in this release. The 3DS version is good, but it pales in comparison to the Wii U release.
The levels are better. Even the levels shared on both versions have a bit more in the Wii U version, like Guar Plains with more platforms and Metal Face appearing, and the Boxing Ring having the aliases for each character, though Wario's isn't so great (he's not all about farting. In fact, it barely factors into his own games, if at all).
Also, Kongo Jungle 64 returns. I've been playing Smash since the N64 days, so this was really nice to see.
The content here is greater than in the 3DS version, and seeing as how the 3DS version already had plenty of replay value, I think it's safe to say that you'll take more than just three months to unlock most of the content.
The roster is the same, and the gameplay is the same, so your skill level will carry over from each version. Good for those who don't want to have to relearn stuff.
All in all, if you have a Wii U, get this game! if you don't, get one as soon as you can to play it!