Not sure what to do about this...
- display all factions (rebels and subjugated colonies of other empires) in the diplo screen, risking making it really cluttered
- make all factions work like being part of the parent empire (for diplo purposes)
I would propose to treat given rebelled system like a new minor race, but only one new 'race' for given empire. Such 'minor' would be treated like every minor race. I believe it would save some new coding.
If another colony rebels they will join existing rebelled 'minor' and create multi-system 'minor', of course without ability to colonize any other system.
If subjugated system rebels, it joins first: parent empire (if still exists), second: existing rebelled faction, third: creates new faction (as 'minor' race) - but to revive the empire is also an option.
All diplomacy would work without any changes, including membership, but with one exception: a rebelled colony could not become a member of parent empire, but instead of that, in the end of the membership process, would be fully incorporated as non-rebelled system. I suppose such situation in game practice would be very rare.
The last question would be about subjugated systems and rebelled systems existing as parts of the same empire. Probably simply to allow that.