I actually think Freespace had more realistic solar system structure in mind anyways. Note that each strategic location on the Freespace strategic map represents a star/solar system (eg, Sol, Alpha Centauri) or other large body, such as the Gamma Draconis nebula. They wouldn't represent planets. I'd expect between 0 and 2 colonizable planets (for the GTA or PVN, anyways) at each star.
I think a better system would be if you made it so that stars or empty 'strategic' sectors, like a system with nothing but nebulae/derelict asteroids/jump nodes show up as red, green and yellow, and make planets into tiny dots like the Galactic UI mod. This would mean that at the typical play level of zoom, it wouldn't be a big difference, but when you zoom out to the level where in vanilla sins, each star has it's little 'galaxy' aura, that's where it should look like the Freespace strategic map. Actually, this probably makes things a lot simpler, since you don't actually have to do anything for the planets or stars themselves, just replace the zoomed out ones. The difficulty will be in having them accurately represent the alignment of the system, and I'd guess in having the links between specific systems show up.
Sorry to just spool out ideas on you guys with no skill to apply them

I was wondering what you were planning to do about incorporating gas (deuterium, I believe) as a resource.
I also think 'borrowing' the ammunition scheme that they're using in the Halo mod, with zero-regen antimatter as ammo. It works a lot better in Freespace, since all the consumable weapons (missiles, essentially) are a lot more on par with each other than the dramatically different MAC and Shiva weapons that they're working on for Halo. Any balance issues could be solved easily by simply controlling salvo size, so dumbfire rockets would fire huge salvos, torpedoes/bombs would fire singly, etc. This means that there's no problem having multiple missiles on different ships, so you can just have multiple missile abilities for multi-role (or selective role) fighters, like having both long range anti-bomber missiles (like Trebuchets) and short range antifighter missiles on interceptors, or torpedoes and cluster/defensive weapons on bombers. Then of course, bases would regen antimatter to act as supply points, and capital ships (only those with hangars) and resupply ships could ferry the antimatter ammo around.
You guys have probably already covered this

I can only think of two points of contention right now. How can you assign a group of strike craft to either a station or a cap-ship (fleet, I guess...), and is there any way to implement shooting down torpedoes without making torpedoes into 'strike craft' and bombers into 'carriers'?
With the first point, I think it comes down to jump range. In the Freespace lore, exactly how independent were fighters? I guess they could probably jump almost indefinitely alone, and supplies were the only limiting factor which tethered them to capital ships. I hope that ammo dependence is enough to reflect this on its own.
In any event, good luck! I'm really looking forward to this.