I have read many complaints about this game regarding being the first to get a non-starter starship. To help alleviate this my local group typically plays that if your non-starter flagship is destroyed then you must choose another starship that hasn't been destroyed to take over as your flagship. Any destroyed flagships STILL count as victory points... you just can't use that ship as your flagship any longer. We have been well pleased with this rule as it has made our games much more balanced. It makes people with better ships think twice before just exploring willy-nilly with no real consequences.
We also sometimes use custom scenarios that players can only diplomacy ships of their flagship's alliance.
Anyway the point here is that I have been encouraged by others to mention this to Bandai in general as a possible new game rules or at least scenarios to put in the actual rulebook.
I don't know if this is the best place to post this so I'm sorry if it isn't. I debated and thought it might be though.
Thanks for taking the time to read and discuss.