Things I like so far:
The Lurg. They are so incredibly creepy!
The Starbases. I like having many places to refuel, upgrade, build ships. It was always such a pain to go allll the way back to Sol. I don't care much for the price of crew but I suppose it's reasonable.
The Syreen: Good. Job. Although, I'm running this game in Windows 7 at 640x480 and there's no Syreen commander in the starbase. Just black. I thought I was cheating on Talana for moment, then I noticed that the text for the dialogue was missing too. It shows up when I recap with spacebar though...
Ideas:
One thing I always thought would be cool is if on planet-fall, the away party might find a sentient, non-star-faring race (or several of them) which would allow Captain to recrew at several points throughout space. They'd be easy to design, no ships needed for melee... just some images of them talking and some voice-overs.
A fuel-making tech. Got Radioactives? Out of fuel? Melnorme sold you this fuel-o-matic thing that turns radioactives into starship fuel. Yippie Kayay!
As long as we're going to throw the ISD into melee just-for-fun, why not The Starship Enterprise-D? Be fun to see how the Enterprise would fare against the mighty Kohr-Ah Marauder

After all, those Earthling Cruiser Captains wear uniforms that are highly reminiscent of late-23rd century Starfleet, maybe Excelsior would be more appropriate for inclusion in Super Melee? Given the popularity of George Takei, we might just get the attention of the Star Alliance by doing that. Make sure you put Sulu's face on the display for the captain

Why, I bet Mr. Takei might blast out the development on his most powerful meme-attracting facebook page. Then we'd have over a million people knowing about this thing.
I'm sure I'll come up with many more interesting ideas. For now - keep up the good work guys! I hope that I can make a contribution to the project and failing that, I'll at very least help you catch bugs and test all your alpha and beta releases until you've decided on your full version and advertise the *sauce* out of this project!