As for that I've been thinking that it would be cool if Rebels could get a new research that unlocks a new ability for their Colony frigate:
Annexation - A neutral planet is bribed into joining the cause, providing their equipment to the player.
This ability would give you the planet, it's structures and surrounding fleet, as well as keep it's current level of structural research (logistic/tactical slots, planet HP etc...) for a price proportional to what you gain (meaning this ability would cost a small fortune in credits to use).
This ability would only work on "normal" neutral worlds (regular planets that are neutral and colonized for whatever reason) and pirate bases, but not on the Vasari Planet. This ability would make it fully possible to play future selfmade maps and campaigns with the Rebels as faction without the mapmaker having to worry about it getting unplayable by the player researching the wrong subject. I also think it's a quite elegant and fitting solution for the TEC.
As for the Vasari world, isn't it stated in the bug traking sticky that this is being worked on/solved internally?