They don't need to remove certain animals entirely from certain biomes, just make variants for each species so that they fit in better. Cows as they are now can continue to exist in plains and the like, cows in jungles can be white with horns, cows in the snow can be woolly brown, and so on. They would have the same drops, the same sounds, and the same AI, but the visual difference would help to make the biomes feel distinct. You can try and collect each variety if you want (for a zoo or whatever) but you don't have to if you just want a beef farm as all cows are functionally the same. It adds variety without increasing complexity.
Biomes were something I really looked forward to when they were introduced three years ago, but they were so half-assed at the time that I was left disappointed. There have been steady improvements since then, especially with the biome changes in the adventure update, but I still don't feel that biomes have lived up to the potential of the concept. If 1.7 is to be the biome update, I'd like them to go back and add some additional variety to the existing biomes, but I fear that all they're planning is to add some new biomes and some new blocks to go with them.