I'm gonna have to say kyogre. You probably wanna know why, right? Well, here's why!
-Kyogre gets 5 HMS where as milotic only gets 3 HMS which makes it a good HM user in battle.
-Kyogre ALSO has a better base attack than milotic, allowing it to have physical moves like dive or waterfall!
-It's primal reversion makes it REALLY powerful and better than milotic in every stat.
-It can take more attacks than milotic can AND dish out more damage too.
So yeah, unless you hate using legendaries, go for kyogre! :3
Hope this helped you! :D