I have this greninja, which is Level 94. I want him to be on my team, but I'm worried he wont listen to me.
Defeating all trial captains will ensure that all Pokemon up to level 65 obey you. Then, defeating Hapu will ensure that all Pokemon up to level 80 obey you. In order to guarantee that your Greninja obeys you, you need to defeat the Pokemon League.
Yes. If you beat all the trials, any traded Pokémon will obey, including Greninja.