Well, there's always the possibility of two different groups.
Like, Pikachu. He's got yellow fur in some spots, brown in others, and red cheeks. The "filtered" part is the yellow fur, which will change color, while the unfiltered parts will stay the same, unless you have a shiny or something.
Mmm. And if they make it into a spinoff (which would be GREAT), they can just leave the filters there... I mean, honestly, the core type changes are what really matter.
But man, just IMAGINE how much expanded breeding would change the game. People would be discussing the best combos, trying to find mixes with no weaknesses and great movesets... gah. What a world.
I just had a weird thought. Say if Johnny's breeding thingy went for dual-types. If you breed it long enough, one of the types will change.
The baby Pokemon will inherit one of it's parent's abilities... so what if we got a Shedinja to mate with a Sableye?
A baby Nincada, which would be Bug/Ghost through the breeding thingy. Evolves into Shedinja. Turns into a Dark/Ghost Pokemon. HOWEVER, it gains the Shedinja's Wonder Guard ability...