For my campaign I had a pirate ship crewed by squid infused with two steel (physique) spikes and two copper (intelligence/memory) spikes. This changed how their tentacles work, made them grow and harden so they could walk upright, and granted them the intelligence to coordinate and act as a crew.
There were also some other terrible things on that ship, like a human with increased intelligence and a high Brass rating granted by hemalurgy. Basically I took him in the opposite direction of a Koloss: tight reddish skin, enlarged head, weak musculature, high skills in Mental/Social Conflicts. He acted as the ship's tactician. My plan was that after the players cleared everything else out (or so they would think...), they would discover this guy, smiling and in a posture of submission, and he would verbally disarm them and engage them in Mental Combat, buying time for whatever other terrible stuff I could cook up. (Let's get real though, I'd probably plan out a huge branching speech for him only to have Varrus push a pickaxe through his skull on the first Beat)
I also made a Villain who was a natural Pewterarm given two steel (physique) spikes before puberty and forced to become a pewter savant. The result was that his skeleton grew much larger than it should have, he gained an inhuman amount of muscle mass, and his skin looked like gravel. Pewter Pete, they called him.
Anyway, good luck with your campaign, let us know what you come up with and how it goes!