I have to admitt i didn't read everything carefully because I lack the time because of work, but nevertheless i want to throw my thoughts in the pot concerning the topic:
In my opinion loosing a battle against bigtime cubers is a win... Stacking with cubes is very expensive. Even if I and my teammates loose it feels like a victory, because we made players spend a lot of cash to hold a zone and therefor supporting qonqr for us.
Yes cubes can be overpowered if you use them right, namely recharge and plasmas. But just to attack local zones or destroy beachheads in local towers. I would suggest to reduce the range for the plasmas, but then I know that there are areas with much smaller zonedensity than Switzerland so plasmas would become useless there.
I think that the devs put a lot effort in balancing the game, and it turned out very well.
I just see one flaw in the system and some very interesting challenges towards the players:
Flaw: Plasmas are for local use; since everyone is local in Atlantis it just doesn't make any sense to allow plasmas and recharge in that may zones or even in any zone.
Challenges: The biggest advantage of a cuber is that he doesn't has to coordinate with others on the same level. To fence of a cubed beachhead you have to act extremely fast and you need to mobilize a lot of players. Therefor we need to find better, faster and more efficient ways to communicate with each other. Qonqr isn't just a game where you have to press on the screen as much as possible per day. It's all about teamwork and strategie. Flawless and fast communication. The way this game is beeing played is changing all the time. We have to adapt to the game and to the way the enemie is playing the game. The devs are actually giving us the oportunity to evolve the gameplay. To be a part of the game and not just to be playing the game.
Outlook: I see a lot of hate in this game, and i don't think this is a problem of the balance in the gameplay. There will always be a fraction winning and another one loosing. And the looser will feel "treated unfair". I would really apreciate to see a event where all fractions have to play together to win. Some sort of a regional or global catastrophy we have to fence of, some thing new and exiting. We would have to get in touch with players of the other fractions to successfully win these battles. This will lead us to realize that actually most of the players are really nice people, human beeings worth to know. And maybe we will spread less hate, I really hope so...