Game interfaces sure don't age well, at least not for complex control schemes. I don't remember unit focusing being nearly as cumbersome as it is.
The mod is cool, it reminds me of the Sacrifice of Angels mod and TOS mod for Homeworld. The biggest single flaw in the mod is the lighting. For some reason they went with semi-realistic lighting instead of the game's, and show's, and movie's lighting. In other words, if you're not facing a lit side, you can't see anything, and it really screws with unit management. It makes the game an eye strain, especially for the dark green Klingon and Romulan ships, even when illuminated.
The second, far lesser of the flaws, is the ship use. It's just personal preference, but the Venture, Starfleet Command fighter, and Peregrine should have been arranged completely differently. I would have used a Danube class runabout as the scout, and I would leave it armed, but only barely in comparison to the fighters. The light fighter would be the armed Peregrine we all know. The heavy fighter would be the Venture.
The third issue is, the ships don't have shields, only armor. I remember the Sacrifice of Angels mod giving ships shields that would recharge, so it's disappointing, and this doesn't seem to have repair ships.
That's all the changes I would make, and for such a huge project, that means it's excellent.
One of the things I really like is that warp is cheap, at only 10 RU per ship, regardless of distance. The only down side is that the ships sit dead after warp for roughly eight seconds.
I also like being able to build pods for certain ships. For the Klingon ships there are no alternatives, so it comes off as pointless, but for the Nebula class it's an excellent feature.