Zazen13: I am not exactly naive when it comes to creating online flight sims.
HiTech
No doubt, I would never even insinuate that you are. You are one of my most highly regarded small shop game developers, followed closely by a company called Stardock and then Paradox Interactive. I also would never expect or even want a developer to react exclusively, in knee-jerk fashion, to sentiments expressed on message forums which are notoriously limited in their reflection of overall player opinion. Take the time to sit and watch the MA, you will notice players choose to congregate in large clusters, this is human nature at work, it is where your product shines. That's not going to be "squeaky wheels" you're seeing, that's going to be the will and desire for certain forms of gameplay over other less desired forms.
Game developers tend to fall into the pitfall of looking at numbers and drawing erroneous conclusions about their community's desires and growth with rose colored glasses rather than direct observation of their behavior which is a reflection of what players find fun about the product or an indication of what they do not find fun. Developers always looks at + growth as a "YES" vote for all of their changes. What they don't see is the possibility that one or several of their changes caused what would have otherwise been a 25% growth to be only a 10% growth due to subscriber losses and poorer new player retention.
As a case in point for your product. Rather than expend programming resources trying to coerce and restrict players in an effort to organize them differently against their nature, modify the game to achieve that in a natural and voluntary way. For example, rather than cap'ing arenas to artificially "spread out" players, more fully utilize the large maps by creating a compelling reasons to spread out a bit by diversifying goals and objectives within the map's strategic context thereby creating more natural focal points of conflict and areas of contention. Your huge maps have enough play area for 3,000 people, we all choose to play in just 3 sectors because we enjoy the high player density and there's really no compelling reason to spread out with the current "mickey mouse" strategic system.
In my personal opinion, the heavy handed approach of splitting arenas and hard cap'ing them is more or less a cop out and a cheap substitute for the implimentation of innovate design concepts creatively composed to use human nature to achieve design goals rather than fight human nature, which is like pissing into the wind. I can think of 43 ways just off the top of my head to encourage more fluid player distribution while at the same time increasing player choices and freedoms rather than inhibiting them. Admittedly I am not a programmer, the implementation may exceed available resources or be impractical in some other way. But, your product is so well designed at its core and the infrastructure is already in place that to build upon it to achieve the same goals you strive for with arena caps would almost be trivial to accomplish from a purely logistical perspective. It seems a disservice to your product and your community to not endeavor to methodically do so as time and resources allow.