So, logistically, let's figure this out. We can cut down on art assets by only allowing Pokémon from the same egg group to breed, which would be the most consistent anyway. In terms of two cross-bred Pokémon breeding; they could either be mules, or the offspring would simply inherit the traits of two species randomly from its parents' combined four. I'd prefer the latter, since that's more fun.
Now, here's the tricky part, and I can't decide here. Let's say a Pidgey and a Spearow are cross-bred. How many evolutionary stages does the offspring have? Two, or three?