My thoughts on this:
I like the direction they are going with the story. I dislike the direction they took with the game play though. 12,000 ships running around? Really?
I agree with the story, it's unfolding to be quite interesting. Hopefully they'll continue it while the game is out, so the political landscape changes as well as the physical?
As to the number of ships, it's a big galaxy out there.
Personally, I would have loved it if you started out as a cadet either as a Federation or Klingon, gone to the academy, picked a branch you wanted (science, engineer, security) and then at level 10 or so, became a cadet. You get posted to one ship with a bunch of other players. As you level, so does your skills. At let's say 30-40 you take your test to become an officer. From there you keep going up. until at 60 you become a captain and get a ship of your own.
People complain what about if my helmsman is gone. You get an NPC to take over for you. Same with security. You can custom make these guys to your liking. But they can also be 'turned off' if your security officer is online at the time.
Soooo what you're saying is that a player (who may somewhat likely be a not a hardcore Star Trek fan) who wants to command the pretty starships (a pretty big part of the appeal of a sci-fi game, especially one like this in such a franchise) has to devote however long it takes to get up to level 60 before even being able to command even the smallest starship...?
Sorry, but for an MMORPG, that's almost suicide.
Now I like that idea for a game, but in the format that ST:O is meant to be, the idea doesn't really work and not just for the reason above. You bring up the point about 'what do I do if I have no helmsman' and refute that, but consider this; what about the players who are on ships whose captains have different aims to get out the game. For example the security devoted players are going to be bored out of their minds on a ship where the captain is just intent on exploring. How will players be able to control which ship they're assigned to?