It has always been an issue, the idea of combat challenge was always to allow players to fly what side they wanted within reason of the sides being even.
In my opinion, your late in the game changes to the reward rules will exasperate the problem. Whereas before, it was a "combat challenge" score, now it's an "axis vs. allied" score within the series. As originally presented, there was zero impact if you switched sides, now there could be. If you want to get one of the top spots, you now have to commit to one of the sides. Due to the limited number of events left (two) it will be very unlikely that one squad can get both.
I guess time will tell, but any of the squads in contention for the top squad spots may be reluctant to switch sides, and that will seriously effect the success of this event (IMHO).
The changes still allow for a pilot to compete for the overall spot and now it allows for allied and axis or even both should they so desire.
True, but you have eliminated the overall squad awards, and split it into sides. It's a lot easier to balance the sides if you can ask a squad to change over as opposed to single players.
Squads can now technically fight for both allied and axis top squad by splitting thier squad amongst allied and axis. (As long as its not being abused, I will be watching.)
Bad move for obvious reasons.
I know some may feel this is just a "sour grapes" whine post, but when you present a scenario, define the rules, we play by those rules, then after 3 of 5 events you change those rules, you can expect at least some push back. The better move would have been to stick to the rule set you started with, then make the changes to the next series.
All that being said, I too appreciate you taking the time to put all this together. I know it's not easy...