I would support the idea of when upgrading a ship to a newer design that instead of overwriting the old ship design it is included in a blueprint as the viable upgrade path. So next time you play you have the old version and as you unlock the new tech you get the new version automatically unlocked for you. Make it a path ship upgrade save. Thus, we can customize exactly how all our ships will upgrade on the path to empire dominance.
I guess I was thinking purely cosmetically--but you are 100 percent correct regarding functional changes. It would be nice to have some manner by which we can create an upgrade path.
The only area in which I think this will become tricky is when players decide to go with a different tech order. For example, if I start in a tiny galaxy, my tech order will probably be vastly different from what it would be in a large (or bigger) galaxy.
So if I didn't research sensors next (which would lead to ShipName M2 from a previous game), but instead I researched beam weapons, would the new ship be ShipName M23 (because M1-22 were used in my previous game)?
Not sure if we could have something like ShipName M2, ShipName M2-b, etc. where the difference from ShipName M1 to M2 (from hypothetical previous game) is better sensors, but in the new game the difference is beam weapons and not sensors (M2-b ).