This ain't one of those "I wish Smash 4 was X" post. This is a hypothetical response to give a reason to something that everyone knows what would never happen. Of course, Smash 4 is the real game. But if it was cancelled for any logical reason... it wouldd have to be for another Smash game.
As for the Wii U/3DS game debate... The 3DS may not be holding back the design for Smash 4, but it's fact that Nintendo could do more with a Smash game developed just for the Wii U as opposed to the Wii U and the 3DS. It's all about design choice. Look at Twilight Princess & Skyward Sword. TP was designed for GC and Wii. Skyward was designed for Wii alone. Skyward Sword could push the Wii to it's limits because that was its design. TP was designed with the GC in mind. It wasn't meant to put the petal to the metal for the Wii. But that is perfectly fine. That was a design choice.
But what that means is that a Hypothetical Smash game designed just for the Wii U would be able to do more then Smash 4 (the game we're getting). Why? Not because "the 3DS is holding it back" but because the design isn't mean to utilize the Wii U's full potential. Smash 4's design philosophy is more about "cross play" then it is about bringing us a beautiful "high-quality, super powerful Smash" game. But design choice in this instance of it is like beauty - in the eye of the beholder - and unfair to call any version of it "wrong". Just like how an opinion can't be "wrong".
There is no denying that the Wii U has a stronger processor and can handle more pixels and renders then the 3DS and that is why some fans (including me to some extent) would want a Smash game that would take advantage of that. But it's totally Nintendo's prerogative to focus on the cross system gameplay and connectivity. So is a possible HD Super Powerful Hypothetical Smash game possible for the Wii U? Totally. Will Smash 4 be that game? No. Is the 3DS the reason? It could be. But I bet the real reason is that Nintendo doesn't want to make that kind of Smash game. It's their design choice. It doesn't mean Smash 4 will be a bad game.
Of course at the end of the day, this is all about what would happen if Smash 4 was CANCELLED. And it won't be. Delayed? I'd bet money on that to be honest. But never cancelled.
I could hope that Nintendo would make a Smash game that was designed more on pushing it's home console to the limits but that's not happening right now.
But I'm not going to pretend that a future Smash game on a Wii U could do more, couldn't render more then what Smash 4 has. That it couldn't hold data for more characters, more stages then the 3DS if the developers wanted to go that route.