Even if Deoxys-S rips up certain teams, that doesn't mean it's uber. Imagine if Weavile/Garchomp/Salamence/Zapdos/anything like them didn't exist, then magically appeared out of nowhere. They'd singlehandedly rip more than a few teams to bits of fuzzy lint that cling to that mesh thing in the dryer at first, but then people would learn how to handle them without centralizing. That's basically what's happening with Deoxys-S now, and although it was before my time, I'm sure something like this happened after the unbanning of Celebi or Jirachi in Advance, and it would happen to some extent if anything got unbanned.