I believe that there are a few main reasons for the perceived differences between Star Trek games and Star Wars games: (please keep in mind that this is my opinion based on my personal knowledge of the games named. I don't play FP shooter games so I cannot comment there.)
1.) Star Wars video games have been around longer (Atari 2600 Empire Strikes Back vs Star Trek arcade game [name?] with the lines only graphics)
2.) Lucas is a much smarter marketer. (First Star Wars PC game was out in 91 (X wing)).
3.) Game pace different. (Most Star Wars games involve fighter based actions. Very fast. Star Trek has always been captial ship combat which is slower paced, more chess than Top Gun)
4.) Star Wars universe is more open to adding phantasy elements. (Star Wars is totally make-believe where Star Trek has always tried to stay a little grounded in "reality". This does somewhat limit where Star Trek can go.)
5.) Star Trek tends to be more an intellectual (no flame intended) pursuit. (What I mean by this is that, where Star Wars games, by there vary nature, have lent themselves to mass marketing approaches. Star Trek games have developed more as paper and mapsheet war games (FASA and SFB). SFB, in particular, is VERY detailed requiring a large amount of time to absorb and it cannot be played by just one person. This is why SFC1 hit so big. You combine the largest and oldest Star Trek game going (SFB) with the ability to play by yourself and Boom. Issues have arisen due to the passion of the SFB players devotion to their game vs playability by non-sfb people and the fact that the game itself was buggy. But even with the bugs, SFC1 was a huge hit by Star Trek standards. SFC2 tried to expand this and did a fairly good job but, again, there were issues with buggyness and purity from the sfb point of view. By this time a lot of non-sfb people were drawn to the games. Here's where we get to the complaints concerning playability with the game interface (controls). Let's face it, most people don't want to invest a lot of time learning how to play a game. Most people want just enough difficulty to give them a sense of accomplishment once they get through the learning curve and can start dominating the game. SFC1 and SFC2 both have long learning curves just by their nature of being based (some say loosely) on sfb. This is where we come to SFC3. It was assumed that there were more of the "short learning curve" people out there than were currently playing SFC1 or 2. Combine that with a new company that writes "to the lowest common denominator" and you get the new interface with the easier controls. You add marketing pressures and that leads to low ship numbers which severely limited choices in the game. You also create a second divide between the SFC1 and 2 players who were looking for just the next step and also you further alienate the pure sfb players even more who saw a tolerable game become something completely alien. Add major insult to these 2 groups injuries with the 3rd installment being very buggy as well and then fuel to the fire with Activision's one patch policy (which they aren't following to well.) and BOOM! SFC3 = worst game of the 3 perception wise. Now, thanks to a lot of hard work by guys like Pelican and Korah, we have a couple of versions of this game that are a lot closer to what was expected. SFC3 had some really good ideas and now with the diversity provided by TNZ and DW we began to see more diversity required in the tactics of the game itself which appealed to the more "hard core" players. SFC3 will never have the racial flavor that 1 and 2 did but it's much better now. This leads us to today. We have 3 core groups in SFC. The SFB group, the SFC1 and 2 group, and the SFC3/newbie group. Each group is passionate about their particular beliefs and that always causes friction. Here's where Star Wars greatest advantage comes into play. Lucas has NEVER let control of Star Wars out of his grasp. It's HIS vision. He has total control whereas Star Trek has been a corporate property for years. There have been many groups invovled with it and each one has had their own view of how it should be. Star Wars doesn't have this fragmentation problem. With Star Trek, every new game always takes a slight to major turn. But with Star Wars it's always just about new storyline and or "check out the new graphics!".)
In summantion (writer hears applause) we are so intense in our passion for the StarTrek Universe that we simply will not allow anyone to mess with our version of it without a fight. Unfortunately, there are many different versions of Star Trek leading to many different camps. Star Wars has always just been Star Wars.
If you have made it this far, thank you for your persistence. Feedback welcome.
<S>