I'd really want it to be the action type (third person character control and the flight of the spacecraft as it is). I would prefer it that way.
But it would also be pretty interesting to see if you can somehow integrate both of the options. It'd probably require more time and effort to develop, but it'd be quite amazing. A combination of third person character control, top-down 2.5D flight, and real time strategy. That sounds great to me.