I used to use the GC controller in older games (-and before that back when I was a wee kiddy, Wiimote and its delicious lack of input options. Ouch.), but since Smash4 I've been set on the Wiimote's Classic Controller Pro attachment. -and obviously because I only personally own the 3DS version, I've been using that, too (Not on Wii U though.). Now the 3DS is problematic for it's own reasons IMO, mostly down to the fact the system is just not as hardy as a controller, but there's certainly no input lag to me. -and I'd say the same for the Classic Controller Pro (That there's no input lag - I personally find no other issue while using the Classic Controller Pro outside of "Damnit, batteries!".).
Though, I will admit, I wish consoles would go back to the old wired controller deal, since wireless controllers have been a pain in my ass for years now as a gamer (Battery costs and/or recharger peripherals... Why not just release official wired options? Jeez...). -and I guess that's part of the reason why Classic Controller Pro feels so natural in a bizarre way - it's wired. Sure it's wired to a Wiimote and that invalidates the whole thing, but from a comfort standpoint... -still applies to me. lol
If a TO banned Classic Controller Pro (-and if I was even really into the tournament scene to start with.), then I would be a bit miffed, but I don't think it would be too hard to transfer my play-style back over to GC controls (Though I remember re-binding buttons to an awkward way regardless. I usually hate using shoulder-buttons for primary functions in fighting games, for example.), and I think that'd be a similar case for anyone who was good at fighting games (Since inputs are something fighting game players just have to get used to to be good anyway. -IMO, atleast.).
I don't think TOs should ban non-wired controllers, since most competitive people don't use them anyway from what I see, but they should definitely give a disclaimer that people who do use non-wired controllers risk a DQ or even a controller choice ban if they run out of charge in a match or complain about their controller (for reasons unknown - I mean, you picked it) too frequently. Sure they come with problems, but all that comes to mind there is "No Johns". lol
Though I do understand why people would be irritated when these issues do crop up (I mean, if someone gets DQd against someone they're blatantly better than just because of a controller issue... Yeah.) - I guess it's just down to the player to make sure they don't, and the TO to punish when these do happen. I feel that as a competitive smasher, you have some responsibility anyway, in that sense to make sure you don't peeve the TOs. It's just common sense. -and on the flip-side, I feel the TOs have to try and be as welcoming as possible so to not alienate potential competitive players. Again, I feel it's just common sense.
Whether TOs want to take the risk of controller mishaps happening and causing a bump in the otherwise smooth (lol, jk) process of running a tournament is up to them though, and I can completely respect their decision either way (Unless they have **** reasoning for it. Like "GC controller is just the best. lol".).
(Semi-unrelated, can you imagine if a new top player came along and was using a Wiimote? How salty would people get? lmao.)