The only issue I have with making different colored chocobos have different abilities is that you get into the whole color=stats thing we had with gear that nobody liked. If you bred for abilities/colors separately it would be great.

Chocobos will probably jump automatically depending on how exactly they will act. If they follow us around while active as a NPC party member they are going to need to jump to get to wherever we can go. Just because they do that doesn't mean we'd be able to jump while on them, though