I only have the 3ds version right now, and since everyone seems to use Wii U at tournaments, I figured that's what I should be using too.
I guess what I'm asking is what happens if I go to a tournament with experience with 3ds only.
You might be OK, but there are some potential issues you could run into:
1. Controller. Tournaments may or may not allow the 3DS as a controller, so if they don't, you would have to find or buy a new controller and adjust your muscle memory to play with said controller.
2. Stage familiarity. Of the legal stages, Smashville, Town & City, and Lylat Cruise are Wii U-exclusive and you would thus not be familiar with the quirks of each. (I think even Battlefield and Final Destination might have different collisions and blastzones between the 2 versions, but I'm not positive.)
There are probably more, but those are the biggest that come to mind. Hope I could help.