Oh, confusion. Quite possibly one of the most infuriating elements in Pokemon, finding the best way to fix the problem is very difficult. On one hand, confusion can be rid of by switching out the confused Pokemon, and it won't be there the next time you switch back in. On the other hand, however, provided that the user of confusion on your opponent's team hasn't been taken out when you switch back in, it is possible to come back in and have your Pokemon re-afflicted. Because of this it's possible to get screwed over, switch out to not kill yourself, then come back in and have the battle to go on repeat. Also, eventually you can't switch out anymore because you have no other non-fainted Pokemon.
Taunt is probably the best possible move to have against confusion abusers. Sadly, even this has it's flaws. Due to the fact that confusion is almost always paired with the ability Prankster, you would need your own Prankster Pokémon with Taunt to avoid getting confused. While these Pokémon do exist, they're not always going to be able to fit in your team. And if they do, or are already on your team, they might not have the moveslot to spare for Taunt.
Yes, there are other ways to get around confusion, such as the ability Magic Bounce and the move Magic Coat for Swagger, Confuse Ray, etc. The most common users of these things, however, are weak to Foul Play, witch is part of Liepard's cookie-cutter Swagpard set from last Gen that I'd imagine most of these complaints are based off of. (That set, for a reminder, is Swagger/Foul Play/Thunder Wave/Substitute) Said set plagued the NU tier of yester-gen for being awfully luck-based, to the point of putting Liepard up for a ban just before X & Y hit. Sets like that are able to take the fun out of a match, possibly making every turn a coin flip more often than not in the Swagpard user's favor.
Of course, Liepard isn't the only Pokemon that's going to have Confusion + Thunder Wave/Prankster, with things such as Klefki having better bulk and typing than Liepard, with all the same things at it's disposal. However, while these sets do exist, not every Liepard/Klefki/etc. is going to be using those sets, making a ban on everything that can use it rather silly. At the same time, flat-out banning confusion also isn't very good, because zero priority confusion moves aren't anywhere near as annoying as a plus one priority ones.
Because of this, I would suggest banning Moves that all they do is cause Confusion + Prankster.
Those are my two cents on the matter. Take with them what you will, considering this is my first post.