...its there up with hating any known religion, but Charlie Stross makes an very good point about why Star Trek isn't a good example of well written and thought out science fiction in his blog entry "Why I Hate Star Trek".
It basically comes down to the fact that Star Trek relies upon "technology" to solve every conceivable problem without thought or regard to what that "technology" might even be - it just becomes a way of driving the plot forward without any reference to the characters. Roddenberry actually stated that the problems faced in the original series should be solved by personal interaction rather than some mysterious "technology". You can argue that Star Trek is pure entertainment, but then you soon get to the stage where series such as CSI, Bones and the whole crop of sci-fi over the past 5 or 6 years use "technology" as the plot the distinction between reality and entertainment is blurred to the point where there is no need for character development because as soon as there is an issue or problem to be solved then some magic computer can solve it in an instant.
In someways the modern Battlestar Galactica series* started well with an emphasis on the plight of the peoples and sociological problems they faced; this along with a good dose of a deeper look into to the short-term tactics of an exodus of a race. Sadly, it too ended in a very unsatisfying
finale (Google Search) with a deus-ex-machina ending...
Unfortunately science fiction based on serious science fact or at least on a strong science basis doesn't sell - a genre that authors such as Arthur C Clarke, Frank Herbert and Isaac Asimov were masters of with 2001, Dune and the Foundation series being the most well known examples. In fact if one has to pick a scene that exempifies this in the modern manner then from the film 2010 the scene where HAL relays a message to Heywood Floyd from Dave Bowman (or what was formerly Dave Bowman). While it relies upon technology (ie: HAL, Discovery, Leonov, escape trajectory planning from Jupiter etc) the whole scene is underpinned with a political crisis on Earth, animosity and lack of trust been two rival crews and the disappearance of the Monolith ... in Star Trek, they'd have just repolarised the quantum flux generator and Picard would have said, "make it so..."
* the original series, shown on UK TV as rival programming to the 1984 during the Los Angeles Olympics was pure brilliance, but I was only 12 then, so it counts a nostalgia now.