Ubers is a ban tier to fix OU, which is supposed to be the most permissive balanced metagame possible. For a few gens, Ubers happened to be somewhat playable. Now Pokemon can be banned from Ubers in an attempt to balance Ubers... But if Ubers can be balanced, why isn't Ubers now OU? It's ridiculous. They either needed to stop treating Ubers like a competitive tier, or they needed to make Ubers the default tier. You can't do both.
Why not? I'm no competitive pokemon expert, but Ubers was originally just a banlist. It's since become a format of its own, but is still very different to other formats; from what I understand it's far more offensively oriented, and the viable list of pokemon in it is relatively small. Just looking at the data from July (using the highest ranked players data) it looks like ~38 pokemon were used on at least 3.45% of teams which IIRC is considered the benchmark for reasonably used pokemon, compared to ~51 in OU. So about 3/4 as many pokemon. And looking at the top of that list, man, there's a few pokemon with ridiculous numbers. In OU Landorus-T has a usage of 32% which seems really high, but Ubers has four pokemon higher (or barely lower) than that. It's not really all that balanced of a metagame, basically - you see the same pokemon pretty often, but presumably at least there are ways to counter those pokemon without using the same ones yourself. Still though, the point remains: They had a way to make the tier reasonably balanced for battling, so that's what it gets used for. The normal rules still apply in the tier. And if most people don't want a tier that's quite so centralised and small, which makes sense, it seems reasonable for the next tier down, OU, to be the standard tier.
As for why Mega Rayquaza got banned, I can't say. Presumably it was too ridiculous for even Ubers. It is still allowed in AG.
I'm not saying I think Smogon is perfect - I feel like they care a bit too much about tradition and avoiding making significant changes to things, and as a result you have rather stupid tier names for the main standard formats, as well as a huge mess of tiers with stuff like all the borderline tiers. I don't really feel like bans happen too quickly, I've seen the process they go through and it's pretty significant. They're regularly ending up with 1000+ posts of discussion and thousands of games of testing in data before doing anything, possibly more.