I remember them mentioning something about a fifth character that could be controlled with the touchpad who could interact with the other players throughout the game (unless that was a different game). That doesn't seem to be a fundamental feature though; it sounded like you can play through the game without using it. (And even then, Smart Glass could probably manage it).
Also, I just don't see that being the case. Not a whole lot of people bought Origins, and that game has been sold across the 360, PS3, Wii, 3DS, PS Vita, and PC. Releasing Legends for only one console (a console just launching this year, in fear) is just going to limit its audience more than anything else.
Ubisoft could easily sell the game on both the Wii U (perhaps touting it as the superior version for the controller functionality) and other platforms. That way, they can nab money from early adopters and hold outs while more people get to experience their game. That's a win-win scenario right there.
Every single video of the game shows things you have to do with the touch-screen. For a lot of levels, it's pretty much integral to the game (even in single-player) and wouldn't work on other platforms. And Smart Glass clearly couldn't manage it for two reasons, latency (it uses Wi-Fi) and lack of buttons.
It's the launch game-effect. Obscure games such as this (that don't usually sell like crazy) tend to sell better because there just isn't much else to pick from. That combined with the fact that Nintendo's audience are fond of platformers makes it an understandable decision.
For all we know, Nintendo could have paid them off to keep it a Wii U exclusive or they might be keeping it as a timed exclusive releasing it to the other platforms (albeit shaving off a bunch of levels because of the lack of a touchscreen).