I can see what you mean, I just think you start to complicate things when you start to introduce Light Side and Dark Side, particularly when it comes to the design of cards and the end results. Plus as you say the Empire would end up with the majority of the ships due to the connection to the Republic, but that only complicates matters when you put the Republic on the 'light side'. I don't think you'll ever get people to agree where the different factions belong. It's very simple with the TFA incarnations of their respective groups, but a bit harder with the prequels because they sort of switch sides.
If the Republic are part of the 'light side' then what about the fact the Empire who are 'dark side' should also have access to those ships? That is a very valid point regardless of the situation. This is why I think they need to cherry pick ships and bring them into the GCW era but permit them to introduce CW era pilots.
I mean, in my opinion, the Vulture Droids and some other CIS ships should go in Scum. Same with the V-Wing as it has been established the pirate groups have used those ships during the GCW era.
Actually bringing the Republic and the CIS into the game fully might be a bridge too far for some players, especially when we consider our friend Turbo. The way to please the majority amount of people is to meet them halfway and 'modernize' the prequel ships within the GCW era a bit like how the ARC-170 for the Rebels work. This would please both groups by allowing the prequel fans to have their ships, while not distressing the prequel haters too much. It worked with the ARC-170, why break with that design ethos?