This is backwards thinking. You're basically saying that before playing a new game you want it to mold into the pre existing format. We should be flexible enough to change our formats for the game.
You're worried about taking too much time? It's the game that comes first. Choosing stages, changing controls (yes this happens between rounds sometimes (players even change out controllers for melee and brawl)), counter picking character, getting water, talking to coaches... all these things happen currently. If tournaments run long it's probably because the TOs aren't running them properly. Basic stuff includes starting one time, enforcing DQs for late people, setting the rules of the tourney appropriately for the amount of setups, and communicating well to the attendees. If you need more time, then you do what it takes to earn more time. That's it. You don't shy away from change because you can't step up and run a decent tournament.
Here's a few new things to consider. Being able to play smash on the Wii U and 3DS will free up space and allow for more setups using less outlets. You may not want to play a tournament match on a Wii u pad, but you can warm up on it or do free play. 3DS free play can exist away from crowded areas. If 50 people show up for a tournament with 2 Wii U setups, then you can have contingency rules that people who didn't bring any Wii U setups can play their matches on the 3DS. This flexibility will be great.
I also think the 3DS IR will be able to beam info to the Wii U game pad. You can do all of your set up in your pocket and then come prepared to the tournament. I also think Amiibos will help out in the same way.