I think we're missing something. The 3DS player would have to learn what stage favors which character and possibly the entire Wii U metagame. We haven't seen all the stages of the 3DS version yet, and with Green Hill Zone confirmed, there's a chance Lylat Cruise and Smashville are in the 3DS version. Both will be viable.
Not everything will be on Wii U, you know. If the Wii U has competitively viable stages, then there's no doubt the 3DS version will have competitively viable stages as well, and if there's "banned stages" on 3DS, Wii U will have banned stages too.
Also, the 3DS version isn't going to be suited for casual players. I don't know how will that be possible. I guess playing with CPUs with Items on is casual, while everything on Wii U is competitive? No, I don't think so. Smash 3DS will be competitive.
Anyway, back to topic. As I said before, this has showed that the 3DS version will be perfectly fine as a viable competitive game. If Nintendo didn't do the tournament, everyone would most likely be hating on the 3DS version still, but it happened. Now everyone's hyped about it, and that's really, really great.