In my opinion, one of the biggest issues, if not the biggest issue, is activity. It seems to me like people would have a lot less of a problem with the fragility of POBs if they had enough people on to put up a decent defense. Obviously people get on when they can, but the greater majority of us split our time between multiple characters, and many people seem to only get on certain characters if there's action for them at the time, and then switch to another once it's over. While that keeps things interesting, it also distracts people from properly caring for their bases, and nobody likes their base destroyed, even if they only occasionally checked up on it just enough to make sure it's still there.
My point is: Seriously consider the activity level of your faction, and any allies able to help build/maintain/protect your base. POBs, in my opinion, should add value to wherever they are built, and should be seen as the centerpiece of any faction that builds one. They should have more meaning, and be more of a factor inRP, rather than just an expensive target for anyone outside your faction's timezone.
Obviously the activity level of the server itself is a different topic, and there are plenty of other factors to consider regarding POBs, but I just wanted to share my point of view.
P.S.-I may have only been here around a month, but I really enjoy this server, and the POB mechanic, regardless of the controversy surrounding it.