I don't know about this. I know TOS best, and in that series we had an intelligent gas cloud, a living rock, several non-corporeal beings (including several made up only of pure energy) plus the Metrons (GOD knows what they are). Only one of these was evil. We also had the Medusans, a very, very ugly race that was very, very good.
I could be wrong, but I like to think that the lower FX budget made for greater inventiveness.
TNG gave us smart sand and nanites. But I agree with the general observation above, that pretty=good and vice versa in all of Trek. (Still, let's also not forget that NBC initially so freaked out over Spock that the network airbrushed Nimoy's eyebrows and ears in publicity materials. He was the original good-but-icky Trek alien.)