I hope nobody laughs this idea to death, but one thing I loved about "SPACE: 1999" is the ability of the Eagle class spacecraft to "dock" with other ships, especially each other, even while still in flight. Another thing I loved was the modularity of the Eagles; the command module could break off and become its own ship.
I'm wondering if there isn't some design that would allow Federation Starfleet shuttles/runabouts to both (1: have sides of passenger compartments exposed so that the ships could dock in space/flight, and (2: have a more modular design so that sections could be jettisoned/replaced for mission-specific reasons.
One idea I've never seen explored in trek is the notion of a shuttle's nacelles being oriented like the Stargazer: one on top, one on the bottom, only long and thin so they span the length of the ship. Another idea would be if the nacelles were closely integrated into an aft compartment, with forward compartments for command/personnel/cargo.
Does any of this make sense?