I'd throw my hat in with the Star Trek one. For one it is practically the epitomy of sci-fi and due to its popularity and huge audience it would be liable to make a very good investment on obtaining the license. Also it would mean that people could finally fight those 'what if?' scenarios such as the Enterprise-D vs the EAS Furies (or the like). As for miniatures I'm sure that with Mongoose's new buisness relationship with Iron Wind they could arrange something or just run off counters for now with a hope of making the minatures in the future should the project prove profitable.
In terms of fleets you've got everything from the Federation, Romulans, Klingons, Cardassians and the like to appearences by the Sheliak, Kazon, and Hirogen. There's scope for further developement and supplements; Alpha, delta, gamma and beta quadrant books and possibly a temporal anomalies source book; time ships, Krenim ship (Voyage:Year of Hell) and alternate timelines such as the three nascels Enterprise and the Aliance ships. Plus it could be split into a post and pre TNG, pre including the Vulcans, Orions and Sulaban and post including things like the Dominion (probably a Jem'Hada fleet with a few points allowed from the Cardassian and Breen lists), Species 8472 and the Sona (Insurrection).
Also as has been said there are a number of fan/player made systems or mods out there, proving its popularity and saleability. Just because it has been done before is no reason not to do it, especially if it can be done well/better and a good bit of profit made out of it.
As for the other suggestions:
Battle Star Galactica wouldn't really work for the reasons mentioned and the fact of only two fleets.
Star Wars unless you're going rally early or really late you only have a couple of fleet options, plus the license fee would be disturbingly immense.
Farscape I don't know enough about to really comment on it but I think the audience size would be abit limiting.
Stargate would be nice to see, but I think it would work better as a Battlefield Evolution game and the fleet options would be rather limited without some 'maginative thinking'.
Traveller (or something else of their own design) the audience potential probably wouldn't be as strong as any of the others and they would have probably mentioned that as it is in house and there's no possibility of a license not coming through for it.
Another possible nice option would be Andromeda, though this suffers from similar problems to Stargate and Farscape, though it would be good to see.