I just defeated the grass gym and Milo told me I could catch Pokemon up to level 25. Is there are higher level cap for obedience if you train your Pokemon? Or does it not matter if I catch a level 26 Pokemon or level up my Pokemon to level 26, will both disobey me?
Every Pokemon of your OT will obey you, no matter what level. Pokemon in the wild above the current level cap cannot be caught, so that part doesn't matter. Getting traded a Pokemon above the current level cap gives it a chance of disobeying you.
Hope I helped!