You could have a menu of forms like:
The 3.5E Player's Handbook 2 did something like this if I remember correctly. You started out with a "predator form" at level one and got some more advanced ones later (flyer, plant etc). This would probably be similar to what I came up with in my initial post, but without the player having to mess with -- and being able to abuse -- the NPC ability system. Not every point of XP spent is worth the same, at lest for combat abilities. Increasing your natural attack is potentially more powerful than e.g. adding Superior Traveler. Never mind that a Flyer costs the same as a Walker, although I'm probably still thinking in 3E terms here, where flying was something you usually didn't get before 5th level, whereas you can get it as a species ability in Fantasycraft from the start (or by spending two feats).
Hmm, given a bunch of templates and the basic mechanic, this is still quite a bit more complicated than other paths. Would this still be acceptable in comparison? Creating a whole expert class for it might be a bit overkill (and wouldn't make it possible for someone to shift starting with first level).