Looking at the unholy terror Mega Rayquaza seems to be since it has an item slot, does anyone think it might be wise to ban the beast from mega evolving if it comes into battle holding an item much like how other megas can't hold any item save their specific stone?
Won't happen. Besides, there is absolutely no reason to force Mega Rayquaza to not have an item, because this is not how it works in the game. Mega Rayquaza is overpowered, just like most of Pokémon in Ubers. This isn't a ground for banning - Ubers without Xerneas, Arceus, Kyogre, Mewtwo, and other broken mons wouldn't be Ubers anymore (yes, Gen4 Ubers banned Arceus, I still think that was a mistake).
Ubers is a centralized metagame, this is by design - use that for your advantage. If you want to play a less centralized metagame, then play any other tier (although, you probably will want to wait for the metas to stabilize after ORAS release, but OU with ban of Mega Salamence is quite playable).
What Ubers ban for is uncompetitiveness - this is why Swagger and Moody are banned, and Sleep Clause Mod is in effect. Mega Rayquaza is not even slightly uncompetitive - you can use it as well. Practically every move you will see on it, with exception for Draco Meteor has 100% accuracy and have no secondary effects that have only probability of happening - so there are no luck aspects involved (yes, I know, damage randomizer, criticals, speed ties, but that practically affects everything).
While powerful and destructive, Mega Rayquaza has checks, in particular Ditto, Groudon, Lugia, and Klefki. In that respect it's similar to other Uber threats. Yes, it doesn't have counters, but some other Ubers threats don't have them either (looking at you, Deoxys-A).
I agree that Mega Rayquaza is so good that it would be stupid to not use one. It's so good that there is no reason to use other megas. Just use it as well. Know that everyone will be using Mega Rayquaza. In fact, it's pretty balanced, when everyone has one. There is still variety, as people can run different sets for Mega Rayquaza.