I love that this thread exists, and I pledge whatever help I could offer (though like many here, 3D scares me and programming scares me more). As a HUGE Wing Commander fan, I have all the games, in various formats, and still have the blueprints for WC 1 era ships from the original set. More than happy to scan them in, if they're not already available online.
My 2 cents:
- The tricky thing about WC is that, since you're a fighter pilot in the game, a lot of the ship classes and combat revolves around smaller ship combat. I don't even know if this is possible in the Iron engine, but if the capital ship experience/power system can be selectively toggled for specific fighter squadrons or even an individual fighter... then you could "hire" Iceman or Thrakkath. And they would have unique upgrades that allow them to torpedo carriers or avoid damage, etc.
Half the fun of playing in the Wing Commander universe is your wingmates and downing enemy aces. Losing Spirit is just as bad as losing a planet. That may not be able to be preserved for a fleet-based game, but it should be explored before nixed.
- Era. I would set this no later than the WC2 era, only because it could spiral way out of control with all of the other factions (Borderworld pirates, Nephilim, etc.), events and not to mention the number of ships increases dramatically and probably makes the project less likely to come to completion. And besides, if you're following the WC1 era at the least, you've got your third side already: Firekkans!