How about generic IDs don't get to fly anything bigger than a gunboat? Change the Merc and Military IDs to reflect this. There is no reason for generic non-aligned ships to be as large as those belonging to fleets with entire governments and several planets financially backing them.
I also like the idea of a player-purchased license that is destroyed when the capship dies. Make the license cost a serious chunk of change and you'll see a lot fewer BSes in space risking their $100mil licenses. This would also reduce the number of ship suicides and perhaps put some cap ships out of action for a while when lost in battle.
"To gain a hundred victories in a hundred battles is not the highest excellence;
to subjugate the enemy's army without doing battle is the highest of excellence."