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I'm having trouble figuring out who is better. I'm also getting a Mewtwo and Rayquaza but whoever is stronger I will use more.
Please help me.

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In-game or competitive? If competitive, what format?
He is getting. Then it is in-game, sumwun

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Mega Rayqyaza is definitely the much better Pokémon.

  • Unlike any other Pokémon, Rayquaza can Mega Evolve without a Mega Stone. It simply needs to learn Dragon Ascent. This means Rayquaza can hold a different item such as Life Orb, Choice Scarf, etc.
  • M-Rayquaza's ability is Delta Stream. This "protects flying Pokémon". In other words, ALL flying Pokémon on the field will lose their flying weaknesses. As for Rayquaza itself, it will be only x2 weak to ice, no longer weak to rock, and resistant to electric.
  • M-Rayquaza has a good movepool. It has reliable setup with Dragon Dance. It has great physical coverage options such as Earthquake and Iron Head. Its signature move, Dragon Ascent, is basically the flying type version of Close Combat, which is a great and powerful move despite the defense drop. It also learns Extreme Speed for priority.
  • M-Rayquaza was banned from the Ubers tier. In other words, it was too overpowered for the overpowered tier.

On the other hand, Mega Mewtwo just isn't as good of Pokémon.

  • Mega Mewtwo X DOES need an item to mega evolve, meaning he doesn't have access to things like Life Orb. M-Mewtwo actually has higher attack stat but this makes up for it and more.
  • M-Mewtwo's ability is Steadfast. This raises speed when it flinches. This is very situational, and who wants to get flinched in the first place?
  • Many Psychic types, M-Mewtwo included, having limited physical psychic attacks. Mega Mewtwo X suffers the most, as its physical attack is higher than its special attack by a substantial amount. The only physical psychic type physical moves Mewtwo can learn are Psycho Cut and Zen Headbutt. Its fighting type movepool is a bit better but not the best, as it can't learn Close Combat and High Jump Kick. If you want good moves, Mega Mewtwo Y is the superior Mega Mewtwo.
  • M-Mewtwo X is in the Ubers tier, and it's there to stay. It's a fine Pokémon, sure. I mean, it has great stats. But it's still not the best, and Mega Mewtwo Y is a better Ubers Mega.

So, yeah. Use M-Rayquaza more often. It is a much better Pokémon.

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This person is "getting them" in game, it seems. V-create is an event only move that they will not be able to obtain. :P
Ok, then. My point still stands. Mega Rayquaza is still better. Whatever, I'll edit it out.
Yeah, Raquaza is definitely more versatile than Mega Mewtwo X.
Thanks.Now I know that I will use Rayquaza more over both Mewtwo megas.