If they did level up the NPCs in Liberty, it would make it a lot harder for newer characters to start up.
The higher level NPCs would only be in the bordering Liberty worlds, as suggested before, and the missions would have to have lower NPC levels as to not make it extremely hard for the newbie in the starflier to make any real money without being forced into slow trade.
most starfliers do not trade anyway they mine in colarado. makes it a pain in the a** for xenos as we is constantly checking levels and we cant do anything when they have xenos in thier cargo hold.
I like ephs idea for weapon classes. i would suggest the same for shield classes and maybe different thruster classes as well.