The problem, as I see it, is that negative reinforcement (such as ENY penalties) work well when you can make an instant corrective change.
For example, if you log in and your team has 2x-3x the number of players of another, then there are ENY penalties. The natural reaction to this is "Oh, crap, I don't like ENY-limitations. I'll go to the other side where I can fly my plane."
However, with the 12-hour limit, someone who flew before work or school, just 9-10 hours earlier, can't switch. They're stuck flying a country they don't really care about, with planes they don't want. Most players will either log off or go play another aspect of the game (GV's, etc.) until ENY either balances out or they get bored.
Fighter Ace had zero time limits on switching and there were absolutely no problems with permanent side balances. In fact, there were less then there were here, especially during off-peak hours.