You are forgetting one major point of using organic trait. It makes your ships cheaper. You can build at least 30% faster and upkeep a fleet far greater than other players. Organic weapons are less powerful, yes, but If I can make Light cruiser in 2 turns instead of 4 (at the beginning of the game) I am going to kick anybody's *** who has temporal, crystalline or actually any other trait because I can have twice as many ships in my fleet in a short time. At least in the beginning.
Organic armor is not that good, I agree, but I add few pieces of it because relying only to shields is utter stupidity. Best protection you can have with at least 11 crystal armor and 2 shields (I am too tired to tell the math inside it, but when using enough crystal armor and shields, no weapon which makes under 150 damage, can harm you).