I have to say the 3DS version got the better deal.
Wii U suffers from redundancy and a lack of variety. We don't need two Animal Crossing stages that both take place on a floating platform above the town, we certainly don't need two Mario Circuits, Kid Icarus doesn't need two stages in Skyworld (especially given that the original is utter garbage), and they couldn't be bothered to change Big Battlefield's aesthetic even a little bit to differentiate it from the original.
We've got only one scrolling stage (and an ugly and poorly-conceived one at that), but FIVE where a floating platform takes you to different areas (Delfino Plaza, the new Mario Circuit, Port Town, Wuhu Island and Skyloft). The 3DS version has 3 scrolling stages, why couldn't they do the same for the Wii U?
A lot of the returning stages also leave a lot to be desired. I mentioned Skyworld already, 75m is...well, 75m, Yoshi's Island is too small and the spinning blocks are obnoxious beyond all reason, and the Shy Guys on Brawl Mario Circuit are incredibly disruptive. And speaking of disruptive, stage bosses are awful and there should be an off switch for them. The Yellow Devil is the worst, ruining Wily Castle by spawning every twenty seconds and taking up half the stage.
Overall, there's barely any stages in the Wii U version I actually enjoy. There are some I'm indifferent to and some I absolutely hate, but very few that I genuinely like playing on. And that's a shame.