So, I had an idea, which could make gameplay pretty interesting, and a bit scientifically accurate. So, adding a constraint (even a minor one at that) to removing structures suddenly, instead of modifying or simply shrinking them. This forcing players to think about how they can adapt current structures to suit a different niche, such as with homologous and analogous structures, or simply making them stunted and less noticable, as with vestigial ones. Such as with forelimbs on large bipedal predators like many theropods, or hind limbs on snakes and whales. Maybe your creatures lifestyle is more suited to terrestrial life, after you opted for wings. So, instead of removing them, you find a new use for them, such as display, thermoregulation, or even developing them into some sort of weapon. I feel even if this feature isn't enforced, or is simply an option, it would be interesting to see it enabled on NPC flora and fauna.
Please feel free to expand on to or critique this idea :3
The whole point of MPs is to account for the time it takes for species to change, thereby preventing edits that are too drastic. To me, it goes without saying that reducing and removing features is no different (otherwise, you could pretty much turn a lizard into a snake in a single generation if you have enough starting MPs to evolve low-friction belly scales).
These are very interesting gameplay aspects I haven't thought about yet ! I'd personally prefer if deleting parts would be completely disabled.
With me I see no deletion as being pretty extreme. It would be very interesting however. :3 I think my idea would be gradual simplification, and deletion. Such as shrinking down, removing some joints, or fingers, say if it is a limb. Bit by bit making it vanish, at a lesser total cost of MP. But I could see an option for no deletion being an interesting sort of 'Challenge Mode' option, to increase difficulty not just for you but for NPC's as well.