I didn't experience the same issue. It just worked. It seems like some compatibility issue.
Drag the folder "Data" and "Graphics" into your game folder, not the folder "Aephiex's Ash-Greninja".
Form 1 is regular Greninja with the ability "Battle Bond" and 2 is the transformed Ash-Greninja.
"Battle Bond" is an ability that allows Greninja to transform into Ash-Greninja after knocking out an opposing pokemon (and revert to it's regular form after the battle ends). It doesn't make Greninja look different before it transforms and you shouldn't have the transformed form outside a battle.
Features
1. Introduced Ash Greninja to the game.
2. Since Ash-Greninja can't spawn naturally in the core series, there are some tweaks on this mechanic:
• There is a 1/16 chance that a wild/gift Froakie family pokemon is created with the ability Battle Bond.
• Froakie family pokemons with the ability Battle Bond CAN BREED and CAN BE FEMALE and the ability Battle Bond CAN BE INHERITED.
Hidden Features (only available in debug mode):
1. If you hold CTRL while obtaining a gift / encountering a wild Froakie family pokemon, it's guaranteed to be created with the