Here's a thought: Something that comes because we can save, upgrade, and obsolete ship designs, and pick different technology with each fresh start.
Ship Design & Selection Suggestion:
DesignTree
The several upgrade paths are because of different technology selections, and perhaps the discovery of some Ancient Artifact that affects ship design.
It would also be handy if we could put a player note next to ship upgrades, as a reminder of why the new model exists/how to get it. "Fighter-3 tech" or "to Counter the new Phong Confederacy Missile Frigates" or some such. That would make a nice mouse roll-over.