I run Greninja for about four months now, and most of the time the Jirachi was useful only against Night March, Vespiqueen variants and the Seismitoad, with the rotation, NM and Toad will be out of the Standard format and Vespiqueen won't be much playable without the Battle Compressor, so I think the Jirachi is not needed anymore since you won't be facing any of these decks and can fill the space with cards that will be more useful in the next format, such as counters do Mega Sceptile and the Garbodor thing.
I don't like the idea of running 4 Rough Seas, but it's a personal thought, and since the format will be slower, the Ace Trainer and the Assault Vets will be very situational, but without the Greninja XY, I like the idea of using Bursting Balloon.
Without the Compressors, getting the Fisherman or even the Energies will be a little bit harder task.
I don't know which meta you will be facing, but without Tool removal Trainers, Garbodor will se a huge space in a lot of decks, so I'd try to speed things a little bit so I could get rid of it easier, so 3 Wally seems nice to me, but Rare Candy will also help a lot.
So, basically I'd change:
-1 Ace Trainer
-2 Rough Seas
-2 Jirachi
-2 Assault Vest
+1 Fisherman
+2 Rare Candy
+1 Steven (without the Compressor, Steven helps to get both a Supporter and an Energy)
+1 Skyla
The other 2 slots you can probably keep the 4 Rough Seas if you don't have trouble playing in your city meta, but if you face tons of Garbodor and/or M Sceptile, you'll probably need some outs, like a second Steven (or a third Lysandre) or even Regice/Glaceon against Sceptile.
Again, this is just my opinion, I'm not very old in the game and I'm still building my own Greninja deck for the next format, but I'm just trying to think about all things I can face and be able to counter them all, giving my piece of help here.
