What about, then, a faction-designated ship with instantaneous personnel transportation? A Stargate (SG-1, Atlantis style) if you would. One end would only be buildable on the faction base with a build limit of one, and the gate could only be linked to one ship (at a time?).
Players could spawn on the faction base, but go to their gateroom and transport themselves back to the flagship or commandship or whatever it is? A balance, of sorts, between the two.
Gate size couldn't exceed 1x6x6 (one block thick, six blocks high, six blocks wide). Only players on foot or really small one-man craft would be able to use it to travel to the ship. The further the ship is from the faction base, the more energy would be required to make the jump while, also requiring a cooldown.