Mega Rayquaza is simply better. First off, it doesn't need a Mega Stone to Mega Evolve, which means you have room to fit another item. It has extremely high stats and the highest base stat total in the game at 870, and its ability Delta Stream weakens the power of all super effective moves on Flying type Pokemon, therefore making Mega Rayquaza 2x weak to Ice, neutral to Rock, and resistant to Electric. Its movepool is wide and varied, you can run many different kinds of coverage moves like Earthquake, Waterfall, and Iron Head. Dragon Ascent is already a STAB Close Combat for Mega Rayquaza, too. Access to setup moves like Dragon Dance can win a game, and it even gets Extreme Speed for priority. Believe me, there's a good reason this thing was banned from Ubers. Ubers is a Smogon tier mostly consisting of the strongest legendaries and Pokemon in the game, and Mega Rayquaza found itself to be too strong for even Ubers.
Mega Mewtwo, regardless of form, just isn't worth using over how much Rayquaza brings. Of course, both still require a mega stone to be used, but let me mention these individually:
Mega Mewtwo X has extremely high stats, an even higher attack than Mega Rayquaza, and the same base stat total of 870, but one of the main problems is that Mewtwo's physical movepool is lacking. It has enough to get through for coverage, especially the dreaded Close Combat and High Jump Kick that hits like a steamroller. Steadfast is fairly situational, too.
Mega Mewtwo Y has extremely high offensive stats but it's fairly fragile. It might have the highest Special Attack in the game, but its lowered defenses means it can't play as versatile as Mega-X or even base Mewtwo. Insomnia is somewhat situational but much more useful than Steadfast as it allows Mewtwo to absorb Spores and Sleep Powders from various threats.
Don't let these deceive you, though. Mewtwo and its Mega Evolutions are amazing Pokemon and most certainly Ubers. but Mega Rayquaza gives the player such a huge advantage just by having it, especially since Mewtwo can often be self-sufficient without a Mega Evolution, while its different forms play to its versatility. So, yeah, run Mega Rayquaza.
If you're fighting NPC trainers then neither Rayquaza nor Mewtwo even need to Mega Evolve to absolutely destroy them courtesy of their amazing stats.
