I actually don't see why this shouldn't be done. I mean, the main reason why this hasn't been implemented earlier was simply that Disco supported the storyline. Now with OpenSP it isn't that much of a problem.
NPCs are annoying, but geez, they always are, doesn't matter if they are in Liberty, Rheinland or Omicron space.
Additional weapon classes can make things much more comfortable. Like, an own class for codenames only, or an own class for Nomad weaponry. Maybe things can get even more extreme and assign one weapon class to every house/alliance/region of space.
As for the ships, just rename the MkII ships to the original ones and buff up the MkI fighters to the desired level. Said before, and I shall add that one (be it the MkI or the MkII ones) of each ship should be replaced with the other in selling locations. Like, the Patriot is sold everywhere where the Liberator and the Patriot originally is sold.