Two sides usually have more problems than three. Luckily, we have a system in place to balance. The problem with that system is it does not really work with the terribly low numbers we now have in the MA. If your side outnumbers the rest of the arena, you have to fly weak aircraft, switch sides, or log off. I think that is fair. It is not fair if your side has 8 players, and the other two combine to 4. The system was designed to deal with hundreds of players, not a dozen. The ENY system needs to amended or adjusted, not abolished.
Two sides could potentially remedy the problem. However, I fear the same problem would exist but on a more severe scale. One side would always dominate and if you force folks to join the low side they simply won't play. Thus, one side will essentially never be able to fly P-51D's and the other will never win a map.