since i got the eon flute i kicked latios out of my party to make room for groudon, it's just so convenient using the eon flute? do you have a flyer in your party?
I keep Latias actually, she's the only one on my team with a flying type move. I'm more comfortable with Rayquaza than with Kyogre, anyways. Plus, MEGA RAYQUAZA.
I always keep at least one Pok?mon that knows fly in my team, with it being Crobat and Charizard in Pok?mon X and Altaria in Pok?mon Alpha Sapphire.
I suppose I could just use the Eon Flute in Pok?mon ORAS, but the animation takes so long, you don't get it until late in the game (and I would already have my team assembled long before that), and for me, it's much easier to just use fly.
I have pokemon that could learn fly but I don't teach it because there is almost always a better move competitively and HM moves are horrible to unlearn...