I like the idea of high score lists But why stop at one list when you can have several? Things to track for each mission would be:
Percentage Fleet (Tiebreak by Honour)
Some kind of score that balances the three above - some kind of (Honour Saved-Honour Lost)/Time
Maybe also track the three things plus number of fighters/frigs/cruisers in the list (and have a World Ranking!) (and a bit of text as name/description) to remind you of how you scored that ranking (maybe even save all the ships and the deployment - not sure how much space that would take…)
You could even give medals/trophies/etc. for making various levels (Gold/Silver/Bronze)
There could also be special challenge achievements for each mission (easy, medium and hard ones):
No fighters (or no frigates, or no cruisers) (or Only frigates/Only cruisers. Currently only fighters is a bit tough due to low fighter limits…)
No point defense
No armour (or no shields. Or no defense at all?!)
No (particular weapon type/particular module type)
Only lasers (or beams, or missiles - focus on one type of weapon)
Conditions could be complicated, like: 100% fleet at the end AND no cruisers.
This would encourage people to build/try different weapon combos - could also be made part of the challenge system.