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.
Mega Rayqyaza is definitely the much better Pokémon.
On the other hand, Mega Mewtwo just isn't as good of Pokémon.
So, yeah. Use M-Rayquaza more often. It is a much better Pokémon.