I think removing nanites might be good for the game. Noone uses any nanites besides the heal tool anyway.
There was simply no real point in nerfing the noob heal and replacing it with nanites back when 2.3 came. The heal has a few conveniences though.
1) You dont need to have ammo, you dont have to reload.
2) If you use a heal anyway, it makes more sense to go for other low lvl psi stuff like shields/dmg boost/buffs)
3) It lasts longer, which kind of makes sense, since 2.3 made everyone's health pool a lot larger.
You would obviously have to give Tanks their Psi back, which also makes sense, since they are the only class in the game that can not skill whatever they want.
In addition to this, I think it would be great to buff low level PPU spells, to make it viable for people to skill/setup in that direction. For that you would have to sacrifice some of your offence, hence you wouldn't be as effective with a ppu buttplug as someone who didnt put any effort in ppu. As reward, you would have it easier to solo pve and pvp.
This would encourage people to not run around with the same setup and playstyle as everyone else, and make the game a bit more exciting in my opinion.