Hello.  I know this thread appears to have died, but I have my own thoughts about what I'd like to see in a new Star Control game...

First, as has been suggested, I'd render the whole thing in 3D but have the game play entirely on a 2D plane, as in SC2.  With all the graphical effects possible these days, the melee combat could look spectacular even in 2D (which is really what it would have to be to be called Star Control, IMHO).  Basically, rather than focus on making everything fully 3D, I'd focus on rendering the best looking 2D picture possible.

Second, I'd leave resource gathering and planet stuff essentially the same, but the larger screens people play on today allow larger fields for the planet lander, scans, etc.  I'd rework the whole planet interface, actually, to bring it up to todays standards.  And I'd have each planet be a sphere rather than a flat map that wraps on the sides.  I'd be tempted to suggest playing the planet-lander in 1st-person or 3rd over-the-shoulder 3D, but then I think that would not fit in with the 2D combat.  And I'd way rather sacrifice 3D resource gathering than SC style melee.

Third, I'd make the planets and moons actually move in their orbits.  They'd move incredibly slowly, obviously, at whatever rate is appropriate given the speed of the game clock.  It wouldn't really add much to the game in terms of gameplay, but I think it would be cool.

Fourth, I'd suggest devoting 3/4 of the space on the disc to voiceover.  Really, the other game resources would not amount to much if it's 3D-rendered 2D (I would think).  And then spend a lot of time and care making the alien interactions fun.  So lots of dialogue (though not long, droning dialogue like some games), and lots of character movement and expression on the screen.  And get quality voice talent, with someone involved in the game's creative process to direct them.  I don't know about you guys, but I definitely play UQM with voice OFF...

Fifth, I'd ignore SC3 continuity entirely.  In fact, I wouldn't call the game SC4 just to dodge this entirely.  I'd call it Star Control: *Happy Campers* or something (not that, obviously).  I'd be foolish, however, to ignore the positive things that SC3 did contribut though.  One of the above posters mentioned ship upgrades for every ship -- I liked this idea too.  Another thing that I sort of appreciate when I play SC2 (or UQM, now) is the ability to autonav to each planet or moon in a system.  And then there's the issue of the colonies.  I like the idea of colonizing worlds (SC2 seemed off with almost no colonies, even if it made sense with the storyline), but SC3's system was basically pointless.  I'm not sure how I'd improve it, though I think I'd want to include it in some fashion.

The main thing to remember when approaching a new Star Control game is what makes SC2 the greatest game ever.  It's not cutting-edge technology at work.  It's the game's incredibly rich, rewarding gameplay with a very elegant design and interface; it's the simple and perfectly balanced ship-to-ship combat; it's the whisical and humourous story, characters, and universe.  Basically, keep it simple (to use, if not to beat!) and keep it fun and funny, and it will be a winner.  An elegantly rendered 2D design would be the best fit for all of this, I think, and it would be a winner with the sort of people who are into this sort of thing.  You know, smart people. 

Oh, one last thing.  I know it sounds a little like heresy, but I think it would be a great fit on today's consoles.  Those dual analog sticks and shoulder buttons/triggers might open up some fun possibilities with the melee, without changing the core of what made it great, plus there is no obvious advantage to playing on a PC (unlike with, for example, hardcore RPG's or FPS's).

Anyway, sorry about the length.  I just really want to see a great SC4 someday...