I don't think you understand the difference between prevalent and over-centralizing. A Poke'mon that almost everyone and their mom used because of its godly typing and virtual 720 BST creating an environment where everyone had to pack checks dedicated to it that all resulted in an oppressive metagame for an entire type of Poke'mon is what's called over-centralizing. That is why Smogon bans things. Not because they don't like it being used so much. I don't even care about metagames fight me and my 6 Mewtwos bro. Still, I understand their house rules because it's a widely used rule set.
It's all a matter of perspective. 6vs6 singles is not, never will be, and should not be forced to be a balanced metagame. There was a time, in gens 2 & 3, where it was fairly balanced... but that time is over. Gen 4 marked the end of the effective "send out a counter" gameplay that Smogonites are still trying to hold onto to this day. Back in gen 4, we (mostly) all accepted it. Gen 5 came along and ****ed everything up. Lots of "old blood" quit the scene. Gen 6 reinvigorated interest in competitive Pokemon, but people are still trying to force the meta into an outdated mold.
What am I saying? Every other meta besides 6vs6 singles has a much tinier ban list in gen 6. 3vs3 singles, double, and triple battles all cope much better with the massive power creep of gen 6. Those metagames are somewhat balanced. Even with a ton of mega stones, Greninja, and Aegislash banned in 6vs6 singles, the game is not even close to being "balanced." No, it's just been forcibly toned down just enough to allow people to continue playing similarly to how they did in Pokemon Emerald, instead of playing the game like it's 2016.
I understand that my viewpoint is kind of radical, and I don't expect anyone's mind to be changed on this overnight. In the end, I have abandoned the old way of playing... and I use an actual copy of Pokemon to do it, which is more than can be said for most Smogonites.
They can have their meta and their simulator so long as they stay in their containment community.