One interesting way to handle advantages/flaws and new tech might be to allow desingers to use "future tech" but with a chance of picking up a flaw. For instance, in a campaing set prior to DS9, a prototype ship like the Defiant might allow a player to design a new engine (with the Narrator), and then check to see what problems arise from the new engines. This is enetially what happened with the Defiant- class on DS9.

This would probably work out to be easier for an TOS campaign, since we have some clues as to what the new tech could be, but it could still hold up for some things in the post-DS9 era. For instance, it wouldn't be hard to figure out SPACEDOCK data for Type-XIII phasers.