I pretty much gave up on the Star Trek franchise after they mangled the Maquis storyline.
http://memory-beta.wikia.com/wiki/Maquis
After portraying them as terrorists over the course of two series, the Maquis was conveniently wiped out off-screen. Then the Federation goes out of its way to liberate & rebuild the Cardassians....the empire that attacked & terrorized the Maquis in the first place.....
Right then, I discovered that the Federation was no better than the Alliance....
I give them a bit of a pass on the Maquis. The "portraying them as terrorists"... I never saw that. They had core characters, like Ro Laren, the Bajoran woman played by the actor who was Admiral Caine in the BSG reboot... and the tattoo Indian guy who was pressed into service as Voyagers 1st officer etc. So they had folks of "good character" coming and going from the Maquis, and I thought they always portrayed them as a complicated gray area.
As in, "The Federation's hands are tied by treaty, and breaking the treaty will start a full-scale war. And blowing stuff up and guerrilla warfare is bad, mkay? But yeah, your grievances at being hung out there when we ceded the territory, and how the Cardassians behave are rather valid. And the Maquis are all rather solid and brave individuals."
I always took away from it, "Everyone's gotta do what they gotta do." Would the Federation really be acting in a responsible fashion if they started a full-scale war over a few thousand people?
Ham-handed as it was, I saw it as STNG, DS9, and Voyager taking a stab at trying to portray some real-world complicated ambiguity, and situations that had no good pat answers.