Hans, Nath is right. There is Starfleet Command (SFC; SFC2; SFC2:OP) that has a lot of the functionality you're talking about. In fact, it features a persistent-universe (customizable by server) campaign, complete with a strat model. Players start out as Lt. Commanders with some small ship and gain prestige. When new ships come out of the shipyard, players have to bid on them.
Anyway, you move from sector to sector, battling the enemies (of the Federation, the Klingon Empire, the ROmulans, the Gorn, and so on), investigating shipwrecks, scanning planets, or whatever (Evidently you can write your own missions). The enemies can be human or AI.
The problem is, as Nath pointed out, it gets boring really quick. Much of this is due to the design limitations of the game.
SFC is a painfully (not to be confused with painstakingly, which it is too, come to think of it) direct copy of an old, grease-pencil and hex-map game called "Star Fleet Battles", originally published in 1976 or so, and continuously updated.
SFB took as its inspiration the original TV series (and gasp, even the cartoon), but very quickly adapted to include the stuff from the movies. The SFC graphics are heavily influenced by the movies.
The game is played in two dimensions (you get 3-D perspectives, but the ships bank and yaw; they never pitch. This certainly makes it a little odd, but since it is true to SFB, it allows them to use the boatload of ships designed and playtested over the past generation.
It's also hampered by the SFB campaign system, which was all about blowin' stuff up.
Oh yeah, and the "Dynaverse" MMP system, while cool in concept and flexibly scripted, doesn't offer enough variation for people to get hooked. In the end, it comes back to the same sort of combat.
And finally, each individual battle/mission can only have 6 human players in it.
1. No, you can't walk around the interior of the ships. Do you have any idea how much art time that'd take? Sure it'd be cool, but what do you want to do with it? As you note, SFC has a lot of ship designs; SFB has even more. Most of these are not "monsters". It's funny, but the *good* players like crappy ships.
2. SFC is prestige only. So, if you've got a group of players together, what do you do? Multicrew a starship? What kinds of missions would you run to make that interesting? What sort of functionality do you plan on modelling?
3-5 are not in SFC2
6. Is
7. Mouse control. Typing's a little over the top for me.
8. My God, do you have a set of Vulcan ears you put on from time to time?
9 and 10 are in SFC2, believe it or not.
So then, the folks who own the rights to Star Trek will say that many of your features are already in existence, and the others are simply not profitable.
In any case, as implied by your post, the big problem with doing anything like this for Star Trek is that people have certain expectations, whether it's TOS, the cartoon, the movies, TNG, DS9, Voyager or Enterprise. The folks writing those scripts didn't care as much for continuity as the hard core fans. And someone's gonna say "this isn't the Star Trek experience I've been dreaming of." Hell, most of them are gonna say that, and they're gonna let it get in the way of appreciating your game for what it is.
You're much better off taking your ideas and building a completely new game. Since it's SF, you can design the universe and the laws of Physics around what the computer can simulate well.