I recently rolled up a navigator and got the regeneration trait as a mutation.

This is a bit of a problem. I planned to go into the Augmenticist alternative class and snag Physical perfection, as I wanted to roleplay an omnisiah / ad mech obsessed navigator, constantly augmenting themselves to get closer to perfection.

Would this even be an option to me anymore? Regeneration causes organs to regrow and the like. If I become mostly machine, it will likely conflict with this trait.

Is there any way you can think to refluff Physical Perfection to aquire it with regeneration? should I just ask the GM to remove my regeneration once I gain a level of physical perfection?

Just want some outside opinions folks. Perhaps I should just abandon ship on the whole augmentation front.

I would ask your GM how they want to handle it, maybe you'll "fluff" get rid of your regeneration by embedding slightly toxic materials in your body to keep your regeneration busy.. Maybe with the right genesplicing you can get rid of the mutation that causes it.

Oh my God, the only character in the world who could GET Regeneration, and somehow be unhappy. I think that the trauma sites, where the two types (organic and tech) meet, would hurt like a *****, but with the right stuff, the regen could be halted, if you could ever want to not heal from injuries. If you cap the bones with hard metal, they won't regen past it, and with regen being from inside out, the rest should fail in that location. It's sort of like Age of Apocalypse Wolverine; he got his whole hand blown off, taking out one of Prelate Summers (Cyclops) eyes, and the force lightly liquifies the Adamantium (I know, it's impossible, but that didn't stop them). The Adamantium resolidifies over the blasted bone edge, and so the hand never grows back (the cells are marrow-based, and thus sealed in. It ached all the time, but there was nothing to be done. The same might work here; if there isn't anything for the regen to base from, it shouldn't happen. Otherwise, you'd need drugs, or something, to deaden the effect, though I am still amazed one would want to, considering how few of those mutations are only beneficial, and that they are the ONLY mutations Navigators can use.

I think I have it pretty close, because almost every person in the Imperium, even the lucky Navigators, seem to get some tech installed, and they don't seem to have any real problems.

I really don't see the problem; just have Strange Vitality also remove inhibitors for augmetic grafting. The body becomes accepting of new augmetics, readily knitting together metallic sinews and nerve endings with those of flesh and blood.