Yeah you're right, for the trainer it's awesome but it's not glorious at all for Rayquaza to have been captured in a simple Pokeball, he is the badass who can stop Kyogre and Groudon all by himself and it could hurt his self esteem, imagine what could happen if he had to face a magikarp caught in a better ball, Rayquaza would just feel sooooooo weak and think "great, first I'm caught into a regular PokeBall meant to capture Pidgeys and now, I have to face a Magikarp who actually lives in a better Ball than mine, I've got no more reason to live, I became weak and useless, more useless than this puny thing in front of me !!!" so, please don't capture Pokemon with balls that doesn't suit them, it could hurt their feelings !
Well, a Magikarp can be captured with an UltraBall in anticipation for when he will become an awesome Gyarados !! And don't judge Magikarp because he can't swim, Rayquaza can't walk and nobody blame him for that XD And PremierBall are for "fabulous" Pokemon like Snubbull or Jynx !!!