What a great game! What a fantastic take on the metamorphosis concept! I did have some difficult spots, but ultimately I could figure everything out on my own to the end. I was patient enough to accept the initially slow movement of the jelly form, but not everyone is like me in accepting some viewer responsibility. The following criticisms are all quite minor but just important enough to mention:
Is there anything that could be done about the perspective on those two hills with the flowers that butterflies use to jump? I kept missing the center of it because I would expect each time that I should be a square lower than was actually the case.
Between the zombie farm and pirate storylines there was a town where interaction with otherwise seemingly normal humans (were they zombies for some reason?) causes you to restart (and it was also good of you to be quite forgiving so as to not issue a game over in such scenarios). The way I first met the swindling captain (that was or was not the same as the figure near that exit from town?) seemed random and led me to wonder if I missed something in the town.
Unless I am mistaken, certain location-defined actions seemed to require using the action button after moving to that location in a certain form. For example, on a planting hole, I could not simply mutate to the Fangroot and press the action button on the spot; it seemed I had to move to that spot as a Fangroot before pressing the action button.
The bat cave would not have been so difficult had it not been for the strange exit, strange in that it did not seem to afford passage out at first, even in bat form, so only after avoiding it searching elsewhere did I try again and succeed.
That twist at the fortress where we must recall the locations of the curiously important-looking crystals was understandable (I cannot blame one for wanting to test our memory), though it was my least favourite part, probably due to the crisis music which got old fast, for me at least. That was a significant motivation for me to want to end that particular quest.
Otherwise, I am quite impressed with this entry! "Protey" is such a great name not only because of its meaning which is derived from Greek, but also because it is an anagram of "poetry". Was this intended?