I think the "-Alternate" system works just fine. If you need to shorten names to make it fit, then do it. Picard - Alternate, Riker - Alternate, Wesley - Alternate, etc. Then you could make a card that works with personnel and ships with "-Alternate" in title. Give them a bonus for fighting Klingons and doing
missions that also have
on them.
I was actually toying around with some cards that would also give Enterprise-C personnel and the Enterprise-C it's own special icon. One was for the Klingons, the other for everyone else. Both played on Narendra III.
The Klingon Objective allowed you to seed the USS Enterprise-C with crew under the mission and changed the mission requirements to
personnel x5. Upon completing the mission your opponent controls the USS Enterprise-C, which you may now attack and earn points by destroying it.
For non-Klingons the other objective doubled the mission requirements and you seed the USS Enterprise-C with crew under Narendra III. Upon completing the mission you may claim the USS Enterprise-C and the card transfers to the ship. Personnel with USS Enterprise-C in title and lore gain the Enterprise-C icon. Ent-C icon personnel may play onto your Ent-C icon ship and all Ent-C icon cards are now compatible with your ships and personnel, and you may download a card I didn't get to (Make Sure History Never Forgets) that lets you place the Ent-C with crew out of play to score points, but there has to be a countdown and opponent can attack the Ent-C to try and stop you.
Just some ideas I was working on. I know it's more complication than we need in first edition, but it was one of the best TNG episodes and for me really still ranks as one of the best Star Trek episodes from all the series. Why not let us waste time and turns playing it all out?