While I wouldn't personally go as far as saying Mega Rayquaza is subpar, my experience with it is that its not super ultra broken like a lot of people think either. Like its been said, Mega Rayquaza dies a LOT faster in doubles than singles, so its a lot more difficult to use effectively. Personally, I found the best use for Rayquaza / Mega Rayquaza was to pair it with another weather mon (I use it with Primal Kyogre personally). I found having that double weather control could really throw Primal Groudon for a loop!
Hell, I remember a lot of people ended up replacing Mega Rayquaza with Mega Salamence to free up a slot for another Uber. Mega Salamence also has more speed and that pre mega evo intimidate, which can really come in handy.
I totally agree with Firestorm that Primal Groudon is the best mon in this format by the way. Its bulky, got plenty of power, excellent moves like percipire blades, and that amazing ability. Hell, theres even a Specially based Groudon set you can use to knock Aegislash off its ass and prevent it from Wide Guarding while a Primal Kyogre switches in!
Theres some funky stuff in this metagame too last time I played it, such as people using Worry Seed Whimsicott to get rid of Desolate Land on Groudon. And that was just during practicing on free battle / the 30 match tournament. I'm sure theres plenty of room for this metagame to develop in interesting ways!