The game is very good but I have to concur on a few points:
Lipsync sucks, ruins some of the believability
Some things get old the 20th time. I finally found out how to get past some of the scripted voice stuff, but it would be nice for example to have an instant starbase dock.
It is a tad short. I thought there would be more missions
Would have liked more save game options, but I guess they had to do it this way for it to not feel even shorter.
Felix sucks with torpedos. There should be more tips in the manual as to how to get them to be more accurate.
Manual control and firing seems to be far less effective than letting the crew do it.
I know they didn't want to make it feel like Starfleet acadamy, but joystick support, and better ship to ship combat would have been more fun.
It seems to me the various camera options aren't very effective. They are ok for eye candy, but it is really hard to get a view or a scanner where you have a full situational awareness. The "radar" is 2d, the map mode is view only. It is very difficult to fight from th outside views.
There should have been more rendered, or even game engine built cut scenese. Rendered stuff is even of low quality and resolution.
I get the sense they took so long to build the game that they realized they were running out of time and had to whip together the story and missions with a minimum of time. Thus maybe expansion packs will really let it shine.
Also, the multi=player seems really lame compared to other games I've played. Everyone picks sovereign classs because it is strongest and most popular...