All HTC is trying to do is make the game fair. I don't think it's fair to throw darts at them for trying to do that. Fairness starts with relatively even numbers of players per side. Two things that muck up the works are squads and countries.
I think it's reasonable to say that most people who join squads do so to fly with them, and most people fly for a country because of familiarity with the other players or some perceived personality of that country.
HTC is trying to shuffle the deck to make the numbers more fair. If the numbers are more fair and the deck is shuffled, you have to play the hand your dealt, just like any game.
I wonder if shuffling the deck using squads as part of the algorithm, instead of them suffering the consequences of the shuffling would work?
The number of active members of a squad is known and also general patterns of their activity, including days and time blocks of that activity. If squads are then categorized by activity (>15 active members during time block A, 10-14 active in time block A, 5-9 active in time block A, etc.) you could probably come up with a pretty good way of assigning squads to a country for week and have the number be fairly even.
What I'm saying is to shuffle the deck with that data once per week. Squads would fly with each other in a country for that week, no changing. Dynamic filling of an arena to further even out sides would be done with people not assigned to a squad. A rolling history and data set could be carried over and country assignment of squads could be self correcting.
Since the entire nature of a "country" is changing from week to week as the deck is shuffled, the "country" loyalty issue goes away. If the sides were even, within a reasonable deviation, no capture or ENY system would be necessary, and I suppose that is the goal of HTC and the players.
Anyway, just an idea.