Okay, a bit late but I'm back.
I've mostly played with the Last Unicorn game, and I've found it a lot of fun. As I've said, I like their character creation, which is both flexible enough to create almost every character imaginable, and at the same time they are very much in line with what you would expect from characters in the show.
In fact, my favourite element of the game was that adventures and campaigns were built to resemble episodes and season arcs, adding to the sensation of playing your own Star Trek series, and not just a game in the Star Trek universe. I think this kind of "narrative" approach is very satisfying for people that are Star Trek fans first and role-players second.
Sourcebooks were good, especially the one about Andorians: awesome stuff, and some of it got used on Enterprise as well. It is a shame that many of the planned books never saw the light of the day.
Gameplay is fast and easy, with a very mild learning curve. Rules are easy to understand and to use. As
Vonstadt said, I would recommend it to beginners.
As for the managing of players and hierarchy, actually we went against the advices of the game and started with fully developed characters acting as head of departments, including the captain. Sure, nobody likes to be bossed around, but we recognized it was part of the game and accepted it. Maybe it helped that we were all grown adults (even if playing a RPG

), from college age up. Sometimes people went against orders: sometimes they get away from it with a slap on the wrist (in fact, on screen Starfleet has been notorious in forgiving unorthodox but successful behaviours in their officers), or they accepted full responsibilities for their actions. We even played inquiry commissions and martial courts, which just added to the fun because they were a big part of the show anyway.
We even played a game where the ship was used as an experiment of species integration years before the Titan came out with the concept.
However, my largest experience with Star Trek RPGs was with a home-brewed system we developed in years ago. It's a highly flexible system that could be used for virtually every setting, from a very fast-on-its-feet game to a very thorough managing of starship combat. In fact, we ended up using much of the FASA sourcebooks because our game master loves the stuff, even if I never actually played the FASA game.
I never played the Decipher game as well, so I cannot comment on that.