There are a few things that never seemed to sit right with TMNT and other Strangeness. One of those things was the idea of characters having independent sliding scales defining their hands, the degree of bipedal stance, and their human appearance.
The signature characters, the Ninja Turtles clearly have full hands (because they have no trouble manipulating tools and weapons), full bipedal stance (because they clearly walk around with no problems), and full speech, but no human appearance (they look like turtles, and there's no way someone could mistake them for human).
But in the Palladium game, these aspects are completely independent...theoretically you could have a character with full human looks, but no hands, and no bipedal stance. This could simply mean they look like a regular person who only ever walks around on all fours and is incapable of using their normal looking hands from doing anything with tools...they couldn't even learn to walk upright or use tools, because Bio-E points don't change over the course of play and mutations are permanent aspects of characters.
I'm thinking of a priority system for mutation aspects. First appearance changes, then hands, bipedal stance and/or speech, then the character's mind...
...that's right, the mind. In the comics and the cartoon, there were plenty of mutants who had bestial urges, some even having completely animal minds. The problem is, I don't know many players who do animal instincts well. So we'll leave our player characters with human level intelligence, temporary effects might reduce the intellect to instincts or savagery, but on the whole a baseline of human thought is probably good.
To pull things back to a more game specific mechanism...
Because we're using humans as the baseline, we start with a character who is fully human (rather than starting with something fully animal in the original game). A player buys away their humanity in exchange for points that allow them to purchase characteristics from their chosen animal (claws, teeth, heightened senses, prehensile tail, fast metabolism, natural armour, etc.), maybe they can buy traits from other animals at a premium, or psionic powers. The first thing they trade away is a fragment of their appearance (drop from "Appearance - Full" to "Appearance - Partial" or "Appearance - None"), then they may trade away their hands, bipedal stance and/or speech (but they may never trade away more than their Appearance level), finally they may trade away their mind (but this must be the least amount of humanity traded away). Each degree of humanity lost might gain 5 points (in keeping with the original system and because it's a nice level of counting to work with).
Think of it as the relationship between THAC0 and target number...some people aren't going to like the reversal, some people are going to find it more intuitive this way, but generally it's the same thing from a different direction.
The relationship of Size Level to Bio-E points generally works out, but it gets problematic at the extreme ends of the scale. It also meant that smaller animals had a much bigger potential for mutation variability than larger animals. I remember a lot of large animals that were reduced to smaller than human stature just to gain the bonuses they should have naturally begun with.
By starting with a human baseline, we avoid this a bit. I understand the game balance issues associated with the costs of size levels in the Palladium system, bigger characters had more SDC/health, higher strength and endurance, smaller characters only gained a speed bonus, but by this stage they were also suffering intelligence penalties due to their small brains.
If we balance out the bonuses and penalties associated with size levels, we can strip the cost completely, or maybe reduce it to a nominal value like one point per size level of variation from humanity (either up or down). Players have a natural tendency to play up their characters strengths and avoid situations where their characters weaknesses might come into play, so if we ensure their is a cost associated with both directions then we stem this from getting out of hand as well.
The other major difference between this system and the Palladium game would be the benefits granted by animal DNA...in the TMNT game all characters automatically gained attribute modifiers as one of the first steps of character creation, in this game, those bonuses would come in the form of adjective or adverb traits reflecting the way the animal acts. A player could buy their animal's bonus traits with their points, or gain extra points from acquiring negative traits associated with the animal.
Once the points are balanced out for each animal, a player should be able to purchase a regular version of their animal with all points balancing out. But maybe it's more fun to give all characters a few extra points to play with, so that they get some psychic powers, natural powers or other fun edges to play with.