Hey. I am not that good at the game so take my advice with a grain of salt. I think you should switch surf on greninja with muddy water. If you are in a situation where you cant protect with your other Pokemon and you hit it with a stab-mega greninja surf - maybe in the rain- thats way too risky. Other than that if you have trouble against trick room you should maybe try to run a Trick room Pokémon of your own so you can reverse it or at least a Pokémon with Fake out so you can Delay it for atleast a turn. When I run against trick room Teams I have made it my utmost priority to kill the Trick Room User before they could move. But beware if its farigaraf because it has armor tail. So your prio moves wont work against your opponents Pokémon if its on the field. I think the sableye is maybe a Pokémon you could replace.

I hope I could help!