Your pokemon will not obey you unless you do the gyms. My pokemon have stopped obeying me at lv20 already since I have been exploring and doing the other paths besides the gyms. Also the gyms dont scale so if you ignore them you'll be overleveled. This game says you have he freedom to choose but you basically have to bounce back and forth between paths in order to progress in a way that doesn't make them boring. Your mounts mobility options are locked behind the titans and there are roadblocks unless you do the team battles.