What would be the point of getting the Wii U version then?.
HD, Gamecube controller, Gamepad off-screen play, different modes, different stages, different trophies, the ability to use the Amiibos when they launch since the peripheral for NFC with the 3DS apparently won't launch until next year, ideally for tournament settings it would make a lot more sense to use the Wii U version so you don't have all these 3DSs trying to sync up to consoles, the list goes on and on.
It would be the same reason they show the Wii U version in so many demos and used it for the Invitational instead of putting the 3DS screen on a big screen - the Wii U version just looks better and plays better.
The 3DS's ability to be synced up to the TV would be for those couple months when we don't have the Wii U version available, or for those who want to Smash Run on the big screen. I imagine it'd be a relatively simple task with all the work they've already done.
The benefit then of the 3DS would be that you could take it away from the TV and play on the go. Bottom line benefit of the Wii U version is that it was designed not to be taken on the go, and is thus more beautiful and comfortable to play.