Highly possible that the two issues have been mentioned earlier, in which case I suck, fail at life etc.
Looking at the coming fresh slate, I've a few ideas on how to improve village life.
Construction permits
One problem with villages is that new members tend to make stupid decisions. And once you build your log cabin facing the wall etc., there is no going back. One way to tend to this issue would be to have an option of regulating construction within the village grounds. Basically LS would be able to grant construction permits (via the new upcoming village management gui, pretty please) to villagers they deem smart enough to place buildings within the village area.
Extending village claim area
Not many people will go around claiming their entire village (or it will take a long time), so the construction permits wouldn't be a foolproof solution. Therefore the village claim area should be extended somehow. Maybe by having the village claim radiate additional authority radius that just enforces the construction permissions, or having fixed "village construction area" that can be managed like the personal claims can.
Village access for gates
Gates and keys are a pain in the ass. And since key management still hasn't progressed, what about having the option to designate the gate on "village access", so that any villager could open and close the gate without the hassle of carrying another key. For suspension of disbelief, lets say that there is a hidden opening mechanism or a guard who opens the gate.
This would hurt the raiders, so to balance that:
a) make gates with village access less secure (someone could observe villager opening the gate and figure out the opening mechanisms, torture the password from captured villager, whatever)
or
b) make gates with village access more expensive upgrade to normal gates
I think those changes would help new cities to avoid some of the mistakes of the ones in the previous map. And make villages less reliant on crossroad travel, as a bonus.