I agree with the above post we need werewolves in this game. I love the ultimate form idea. It's a very unique idea that I think will only help the game.
I think with these ideas however you're going slightly against the equal battlefield idea between players. If you assume anyone can use them or infect themselves then it's not a problem.
I wouldn't be against having places in the world where players can venture to set augmentations via naturally occurring monuments or ancient technology. I'm not 100% sure they'd be useful though to the game or if they can be balanced so there isn't a 100% best configuration. Role specific augmentations would be more ideal. Like have an animation for a player touching a monument in the world that reconfigures nanites particles that float to the player (with a cool particle effect).
Heavy Weapon Strength Monument: Decreases recoil by 20% on Heavy Weapons
Lock-On Monument: Decreases Lock-On by 20%.
Cloaker Boost Monument: Increased invisibility while running while cloaked.
Vehicle Boost Monument: Links stamina with a vehicles boost or shields for a 10% bonus while stamina lasts.
...
Basically these would be role choices that go with a player's role. Meaning that there's a drawback and advantage to each one with no single ability that is the best. Some of the ideas the OP listed go along with this. I think they should be 100% passive though.