Undecided!
That being said, currently the working idea is a Lyrical Nanoha-esque space-opera-with-magic setting. Original, probably. Magical geometries, possibly very human aliens, possibly very not-human aliens, space combat with spell cannons, all sorts of good stuff. Aims include: being more fantasy than Lyrical Nanoha; being less fantasy than say, Spelljammer; having space combat that is A: interesting, B: reasonably logical given the rules of the setting whatever they may be, and C: not obviously dictating the lore of the entire universe in order to ensure it looks like 18th century naval warfare cough Honor Harrington cough. Obviously, USEC_OFFICER volunteered to worldbuild, though I haven't shared these details with him yet. :U
Hopefully, the same 'universe' or at least the same set of metaphysics and such can be used for both threads. Thread A would have all the space opera, sci-fi-ish stuff, while thread B would be more of a low fantasy thing, set on a vaguely medieval world as opposed to across the interdimensional stars, though with plenty of lost relics and such to keep things exciting.
The current Alternative Plan
(TM) is to have a Gaiden-style setting, though again, the more scifi thread would probably be focused on Lyrical Nanoha because muh dimensional sea, etc. Not so sure on what the more fantasy half would focus on, or if that duality even makes as much sense in this sort of crossover setting thing, but despite the many unsolved questions, it's good to have backup plans, so for now, this is Backup Plan #1.