Rayquaza is just too cool
Catch him with a master ball and it will look cool when you enter him in the battle!
(Also, if you use the master ball on rayquaza you will have a hard time catching latios/latias)
(I caught latias with a poke ball)
If I were to do favorites, I'd go with my favorite from years ago; that'd be Rayquaza, as it not only had intriguing stats and moves, but something about its abilities made me feel excited. That was especially the case in Emerald Version; not only did I get to capture it with a Master Ball before the 8th gym, it was at level 70 to boot! I knew it was going to be amazing on the team, but also took care to have a good team if not better in general so as to get to and beat the Elite Four and Champion.