Introducing a Challenge Cup tier or unbanning evasion and OHKOs in Ubers should fix this.
Both those ideas are bleh (not trying to insult you, just putting out a counter argument). "Challenge" Cup is all about who pulled a better card, and while yeah, how you play is just as relevant as other types, The levels are random, and you can get NFE's. Which is stupid, to be honest. it makes it a much more casual game play, and giving it a tier takes away from its causality. I dont want to play an Uber metagame that has Minibliss on every fucking team. I'll cry.
I'd say adding in what the OP said would solve issues, but apparently they have it already, and its still not working, inwhich case revisions are necessary. If you have gen 4 pokes in VGC '11 you shouldnt be able to play VGC '11.