Except when your ship is destroyed, that is, then you can instantly travel half a galaxy.
Yeah, it's the gamey-est part of the game. At this point FD should just tell us "yeah, PF-tech clone stuff" and most would say "okay cool, back to game".
I don't support OP's suggestion though, it's too "character-switch" feeling; still gamey, but with better avenues of redress using other system additions. I'd much rather see the travel and ship-delivery services added to solve the per-pilot ship issues, along with an actual set of other CMDR slots for the rest.
More slots gives OP pretty much what he wants, aside from having to work each pilot's progress separately. Three slots would cover a good amount of playstyles; I can't be continually involved in galactic politics and go clear across the galaxy with the same pilot. It'd be nice to have a large range of potential gameplay available at any given session, based on what you've done with your pool of CMDRs.