I haven't exactly been here too long, but I voted III because while it might be the harder option to implement, it does provide lots of possibilities.

I mean, let's say that as with most things, the ship fusion isn't exactly executed without a hitch, so instead of the legendary Super Ship, you instead have a bigger ship that looks like one just rear-ended the other at speed. The bridge for one ship could turn into a stand-alone communications suite while the bridge for the other expands to fit the size of the new ship, rooms could be repurposed and readjusted to fit the new configuration, one cargo bay could end up re-purposed to just a shuttle hangar, and more importantly, none of it goes smoothly and everything's buggy as hell. At least for a while.