Those are some nice ideas IMO. Would be pretty awesome starting out with an egg, and ending up with a badass Mirelurk King or Hunter. I didn't use the dire wolf or deathclaw mods so it seems I missed out there.
I am pretty sure they are used in the chemistry station for some of the crafting recipes there. They may also be used for some armour, but I'm not 100% sure on that.
I actually came across one NPC with missing legs. Only one though. I won't mention who or where they are though since some would consider that spoilers. Either way that would be a pretty nice addition to the game. It'd make the wasteland feel more harsh (as it should).