First of all, to be devil's advocate to some of the responses:
In response to the mention of guilds dominating: Yeah, but... wont it happen reguardless? I mean... even if you can't necessarily "band together" you can ignore someone's space. If there are 3 players in a match, one is going to be unnecessarily ganged up on.
In response to a mechanic needed for Skirmishes: It will happen even without a mechanic designed to allow for skirmishes.
As for the OP: So your getting at, a No-mans land between castles basically, where anyone can build stuff. What about there are neutral structures that can be taken. It would work I suppose: I mean, this is what C&C did a long while back with their Red Alert series, netural structures that when taken allowed for bonuses and stuff. As for Balance, if the structures can be readily taken over, and say (In response to Kire) someone steals them all and leaves, well... they can be taken over by someone else. Put a flag on them and their yours. They could provide situational bonuses, enrich the surrounding terrain and perhaps add a bonus or two to long term things like resources or supplies.
Ex: Watchtower Outpost. One tower, with a small wall around it. You take it you get a view of the surrounding terrain, and you have a few archers that can sit up in it and pluck arrows at greater range.
Doesn't really throw balance off wildly but it could be useful from time to time. And, lets say you sprinkle them throughout, or even allow heros to put them up with help? That way they could be disposable structures that act more like special effects. As long as their advantages make sense of course. For instance: Don't make a single watchtower give you full view of half the world map, that would be silly, give a range greater than that of your city towers... so your guys can see beyond their firing range and have time to run if someone approaches.
Of course you can also put creeps to guard them. So, powerful stuff is guarded by a necromancer and 300 skeletons, a watchtower is guarded by 1 guy in a wheelchair and his sockpuppet. Also, if someone logs off, the structures go neutral again after x time, so as to take into account crashing and whatnot.