Using transformations in other levels sounds fun. They had that in Grunty's Revenge. They didn't really go crazy with it, but that could be really fun. Maybe you'd have to unlock the transformations in specific levels, but then you're free to use them anywhere.
Also, like I mentioned before, what would happen to Laylee when Yooka transforms? You can't use the excuse of her being cooped up in a backpack the entire time, so she could be a second part to a lot of transformations.
Also, yes to secret hubworld transformation and a few non-animal (or at least, non-tetrapod) transformations.