I agree the Fasa Trek system had some merit, if nothing else as a set of instruement panel based ship forms that depend on the ship's size. Keep in mind most small ships only need one pilot though, and we never really delve into ship positions as we do in Star Trek Personally I would almost prefer if they limit ships to Starfighers and shuttles for any real detail and reserve big capital ships for a bigger game. (ACTA or SFOS) or perhaps sell the phip system seperately for those who intend to run life on a ship kinds of campaigns.
Minis, I personally would be fine with a CMG set up ala D&D miniatures as they work well for both skirmish gaming and roleplaying, but I am sure players would argue my logic here,
I applaud the decision to go OGL, but please keep in mind that this also gives you a chance to really tweak the rules and make things more attuned to the B5 universe (rather than a D&D afterthought like Star Wars and Spycraft) take a page from green Ronins Mutants and Masterminds (not that I am saying copy thier revision, just that it is a good example of how much you can alter the d20 engine make an excellent game that feels both unique but still has enough in common with the original game to not feel alien.)