What would be wrong with a transport category, listing cargo or troops as a measuring unit.
Sure, but why score it at all? It's silly that base captures improve your score and resupply runs hurt your score. If someone takes the time to do the tedious but very useful chore of resupping strats, why punish him or her in score? Likewise, why punish someone for bringing GV supplies to friendly players? And why factor in base takes at all? Carrying the troops is more than adequately rewarded by perk points, and it is the LEAST skill-intensive task of taking a base. Just have a troops/cargo flight category that, like ship and field guns, shows up in stats but doesn't effect your score.
I absolutely agree with Lusche about fixing the damage score. The thing I hate the most about the current system is how low the values for ships are - they should be worth MUCH more than town buildings or hangars, because they're much harder to hit, more likely to be defended, and above all must be bombed from fairly low alt which makes it much, much easier for enemy fighters to get to you. Town buildings should be worth the least for the same reasons - they're pathetically easy to hit, less likely to be defended than anything else, and can easily be bombed from 30k where, away from the strats, no one (aside from the odd gastropod) will be loitering around in a fighter waiting for you.
As for ENY, doesn't that already factor into kill points? It seems to me the easiest way to weight it more heavily would be to change kills/sortie or kills/time to kill points/sortie or kill points/time instead. Or eliminate some of the useless score categories like hit % (your gunnery is already quite well represented in the other categories - you can't kill what you can't hit) or above all kills/sortie (I don't see how rearming vs. replaning makes anyone a better pilot). Or do both: make fighter rank the sum of k/d, kill points, and kill points/time. if you want to factor in enemy/friendly ratio, that could also be made to affect kill points.