I remember the capture order system. That was very horribly implemented. It was very obviously going to fail as it felt like they really didn't put in any thought into how to make it work. They just threw it into the game with no thought, saw it fail (as it was bound to in the state they introduced it as), and got rid of it for good. The idea is a solid one that can work and other games have made it work. Planetside 2 is one such game. However, I don't think the system would be good for Aces High. The great thing about Aces High is the freedom you get. Free to fly what you want (almost) whenever you want, attack whatever base you want when you want, or go and do anything you can think of.
I think a lot of the problems we're having right now stems from the low numbers we currently have. It looks to me that the majority of players currently playing in the MA are the base take war winning type, closely followed by GV guys, then dedicated bomber pilots, and lastly the fighter pilot/furballers bringing up the rear as a tiny minority. Base takers want to take bases and win the war in the least amount of time with the least resistance. Best way to do that is NOE raid undefended bases and with the current numbers that's pretty easy to do. There just aren't enough players to go around on the larger (and some medium maps even) to defend everything. The majorities in this game (base takers) are too busy NOE hording undefended bases to defend their own bases, GVers are all in TT or at some spawn camping it, bomber pilots are on hour long runs to strats/HQ or bombing towns/bases, and there just aren't enough fighter pilot/furballers left to do everything. I think if we can get more players into this game, get the numbers back up to at last 500, then a lot of the problems will start go away.