Pretty much agree with Ame about waiting for X&Y. Who knows, Gen 6 might bring so much OP shit that those 3 might be needed to balance it out, doubtful, but it could happen.
That aside, and just talking about those 3 in general. While it can be argued that they can be dealt with, the checks and counters are very limited in terms of ones that work 100%. Examples being Ferrothorn for Kingdra, Skarmory for Excadrill, and Tyranitar for Chandelure. The latter requires something to die, or the best case scenario something has a shed shell, like if you have a Skarmory or Ferrothorn to bait it. While I can't really defend Kingdra and Excadrill, and I really hate Chandelure with ST. I can at least think of one good way to keep ST Chandy in Reborn without a ton of complaining. That would be Team Preview, or making Wi-fi battles on Ladder, maybe both. If people know the opponent have a ST Chandy, which on Reborn, everyone would, then they would be much more careful with the things on their team that Chandy can easily trap and kill. I think the main reason ST Chandy is so OP is because no one knows when someone is running it, and it makes it very easy to trap and kill. Regardless of any of that, I do think these 3 make the meta game overcentralized, and prevents creativity because if you're not trying to defend against it, you're abusing it. However, we also have Clear Skies, which Wolf up there mentioned. That was the solution to SS and SR abusers. People begged and pleaded for it, and yet no one battles in that tier. It was literally active for a solid week at best.
TL;DR: ST Chandy can be nerfed with Team Preview and Wifi battles, and if you battle in CS, the weather abusers aren't a problem either. Chandy is nerfed, no OP weather, everyone wins and nothing gets banned!
Anyway, that's my say on it. Maybe once X&Y rolls around things will be better. Who knows. Peace.