Well, most of it, really. More specifically:
I disliked the lack of continuity: not in the “Hey, last week Tachyon radiation was deadly, now it’s curing diseases!” sense of the word, but in the way the characters never really grew or changed, relationships remained largely static, and the state of the Federation was never radically altered, even if events in an episode would seem to call for it. This was much improved in DS9, but still wasn’t up to the standards being set by Babylon 5 or Buffy: The Vampire Slayer. Consequently, I never grew much of an emotional attachement to the characters: I never cared what might happen to them because I knew that nothing ever would happen to them.
Incredibly unimaginative aliens. Not only did they all look like humans, but they all acted like humans. Actually, alien species would act like one facet of human behavior. Humans can be logical, or impulsive, or greedy. Vulcans are only logical, Klingons are only impulsive, Ferengi are only greedy. Consequently, I never found any of the alien species particularly believable, even on the individual level. Again, DS9 managed to correct this to a certain extent, in making Cardassians and Baijorans able to exhibit the same range of emotions as human beings, but in the process lost any hint that these were actual alien beings, and not just a collection of circus freaks in space.
Total lack of ship discipline. I know that Star Fleet isn’t technically a military organization, but it’s the closest thing the Federation has. These guys are a joke. I remember one episode where some alien diplomats are trying to learn about emotions, and one of them provokes Worf into a fight so he can learn about “anger.” It works, Worf flies into a rage, and gets in a big fist fight with the alien. This happens, IIRC, in the middle of a poker game, with Riker (Worf’s superior officer) sitting right there. And Riker watches them tussle for a good thirty seconds before intervening. And all he does is speak sternly to Worf! Imagine if a sailor on a US Navy ship took a swing at, say, the visiting ambassador from Japan. I don’t care how much provocation he was given, he’d be bounced right out of the Navy and into the brig. I always wanted to see Picard act like a real captain. Not just in giving rousing, vaguely Shakespearean speeches, but in having to occasionally come down hard on his subordinates. Almost never happened. On the other hand, Firefly, in it’s tragically short run, still managed to make this sort of tension between command and crew a regular part of the crew’s dynamics. And that was a pack of smugglers, not the flagship of an interstellar government!
No sense of what life was like in the Federation if you weren’t in Starfleet. No politics, no civilian life, no international tensions. No religion. This one, at least, DS9 addressed and got right. The setting helped: the station was primarily a civilian outpost, so the characters frequently had to deal with civilian issues. There were rogue elements in the Federation government that were often working at cross-purposes to the main characters. The fairly detailed belief system of the Baijorans. The whole dominion war and the hostilities between Cardassia and Bajor. All this, for the first time, made the Star Trek universe seem like a living, breathing creation, and not just a passion play with bad props.
