I'm running into the same thoughts as I'm painting the 'Nids that came with my BoM set. Right now I'm just basecoating them with the black, then going back to the "skin" with leather brown.
I want to keep the armor predominantly black, and the skin/flesh the leather brown. I'm thinking of skull white for the claws/teeth, or possibly boltgun metal. (I know it's wierd, but white claws make me think of either keratin or calcium, neither of which is going to scratch power armor.)
I'm not sure what to do for eyes, (was thinking blue) or for the "dry brushing" highlight.
I'm trying to make them look like animals more so than genetic chameleon freaks.
I'm also trying to think about what to do with the "pockets" in their arms / legs (the ribbed exposed parts). I'm not sure whether to paint them brown and ink them with black, brown and ink with red, leave them black and ink with red, leave them black and ink with brown, etc etc. Right now I'm avoiding painting them.
(when I say ink, for the moment I mean watering down the acrylic a hell of a lot.)
Kinda silly to fret over it I guess, I'm not sure I'll even wind up getting a nid force together when I finally settle on a real army to play.