not going to lie. tl;dr. and saw T3 and instantly thought ... EVE Online.
also after i went back and read your post. I wouldn't think of the ships as in "Tiers" per-Se so much as "generations"
why.. because "tier" implies that tier 2 is better than tier 1 and tier 3 would be better than both tier 1 and 2. in most if not all ways. and the game does not work that way. (at least in this Alpha build)
i believe your "non organic" crew would work better as either a hull mod (AI controlled ship for huge OP hit) or as a separate form of life (Silicoids from Moo2) or (Horta from star trek
http://en.wikipedia.org/wiki/The_Devil_in_the_Dark)
your suggestion for extra crew levels is interesting but i would wonder what kind of EXP you expect each member to achieve for each level there. currently its at 0 xp green at 250 xp normal at 750 xp veteran at 1750 xp elite. and it currently takes quite a while and some luck getting elites without purchasing them.
also to be critical
i would say
green (untrained)
trained (graduated basic training)
regular (been in the service for a short time possibly deployed or not)
specialist (extra training after boot camp in a certain field likely been deployed)
veteran (seen his fair share of battle)
expert (you follow what he says when he says it to the letter if he says jump you ask how high)
elite (leader of the experts "commissioned officer")
Godlike (so like... im impervious to bullets.. WATCH THIS... AKA you.
OR high ranking officer)