All the ships are supposed to be second hand, at one point there was a thread running in the DDF that was positing unique quirks and foibles being part of all ships, due to age, repairs, modifications over the years etc.
i think that's possibly where the idea for engineers originated, while supposed to encourage individuality within the game all that happens is players use the meta game to min/max their stats, personally i would have preferred to have several ships of your chosen type available in the shipyard when making your purchase, all with slightly different stats and bonuses/weaknesses, the bigger more popular stations would have had more choice (and possibly better ships) than the smaller, more out of the way places, although you may still have been able to turn up a little gem of a ship by chance.
You could have a ship that had issues with hard point deployment for instance, maybe took twice as long to deploy weapons due to ageing circuitry but that same old and bodged circuitry somehow was improving the target lock for gimbaled weapons, or a ship that had a fault with it's thrust vectoring so it turned slower to port than normal but could turn much harder to starboard, or maybe the ship had iffy power supply cables to an optional module slot so that occasionally that module would switch off by itself but it also gave you an extra 5% power from your powerplant.
There are hundreds of small variations that wouldn't have made a huge difference from a gaming point of view but would make your ship FEEL unique to you.
The falcon is one of (if not the most) popular ships in scifi and it's mani charm is the fact that it's not perfect but to make up for its reliability issues it's FAST, carrying those kinds of ideas into this game were promised, instead they got dropped and we got CQC, Powerplay and engineers.....