Should have been used more (and more intelligently, as in the case of DS9), maybe, but underrated? Bearded Spock from the alternate universe is often brought up by even non-trek fans, and even those who disliked Enterprise often acknowledge In a Mirror Darkly, as being not just good Enterprise episodes, but good Trek. I think a lot of people like alternate universe stories where main characters are evil instead of good. That's why you see it so much in sci fi. Personally, I think the Viidians from Voyager are underrated villain species. In fact, I think they are a missed opportunity to make they the main bads, instead of the Borg.
The Sheliak and the Tholians. I love non-humanoid races with attitude. Both had powerful technologies and a strict code of territorial rights. The Sheliak were supposed to get a cool exotic ship but they ran out of time/budget and ended up just adding some parts to the STIII Merchantman.
Another vote for Tholians and the Gorn. Even something as simple as a tholian ship docked at DS9 would have been nice.
Chameloids. Shape-shifters of legend and rumour, with who knows what agenda? They could reignite war between the Federation and the Dominion for their own benefit.
Humans. After our history on this planet, are we *seriously* expected to believe that ALL of humanity is just one big happy family? I know we get plenty of isolated human scoundrels and such, but it really seems to me like somewhere some of the human colony worlds would have bound together in a separate political entity with its own agenda that might conflict with Federation values.
True, but the Maquis aren't quite what I'm talking about - they were Fed, really, just operating independently because they couldn't get the Federation government to go along with their aims. I'm talking about a group of colonies that want nothing to do with the Federation - racial or cultural purists, human isolationists, extreme libertarians, or some other ideal that just doesn't jive with the Federation. Australians that disagreed when their country finally joined the Earth government.