A few ships saw regular use by both sides, especially with the Rebel practice of liberating ships from other forces for themselves. Shared ships commonly referenced so far include:
Dreadnaughts
Nebulon-B
CR-90
Any others?
If we were to see these and/or others, how would you want to seem them implemented? Just new cards/bases or entirely new models with repaints? Imperial ships could obviously look cleaner, more pristine than Rebel ships. Maybe they could even have slightly different stats, Imperials having better stats to reflect their greater resources for crewing them and Rebel ships having more flexability to show their independent style? Title cards would also be a great opportunity to distinguish such ships between factions. Or would you rather both factions have zero overlap?
And what about "captured" Imperial ships for the Rebels, like a pock marked ISD?
Personally I'd be okay with some overlap. But in order to allow each faction to retain their unique identities, I'd maybe say the secondary faction "owner" would only be allowed to field 1-2 ships that were not of their own origin. That would keep the Imperials from finding Rebel forces entirely made up of Imp ships that would ruin the feel of the game. It would also make the presence of a ship of Imperial origin in a Rebel fleet feel properly "stolen" on the other side of the table.