Well the idea with controlling the gates is that you try to take over the gates controlled by other factions for ease of access, movement denial and resupply purposes. Because the 'city' would be incredibly large, it would be good to store supplies inside fortified ruins or hidden bunkers when the factions start getting close to the interior of the 'city' due to the time it would take to /f home then teleport to the faction 'lobby' we could call it - a small base or square outside the warzone with no pvp - and then traval all the way back inside the city. (Not to mention having to fight mobs, defuse traps that could have been laid/take a long route round/escape or fight off ambushes)
This means that faction would have to scout out the supply bases to reduce the fighting ability of their opposing factions. Smaller factions will probably mean less stuff which means smaller bases, these being harder to find - so in theory the system should balance itself.
If a faction foregoes the use of supply bases, they're supplies either have to be stored inside gatehouses (which are major targets), hidden chests which is impractical or have to wait the 10 - 20 minuets for a few stacks of arrows/fresh armour, risking the supplies being lost in an ambush, being destroyed by mines or lost to mobs.
Either way, you still have raiding bases and raiding players for supplies, it's just that it is optional for the faction. If a supply base is found, you can have all the scouting, planning and preparing you want before finally going at it. At least that was what the original idea was attempting to get across.
But a problem I thought of would be map making. Perhaps we could all make the it together (the admins adding secrets, adjusting things with plugins, ect) and then it would be fairly balanced as everyone would know a little bit about the map.
@Dannie: The bonus of capturing a zone would be ease of access through owning a gate and quick resupply (though nothing would stop enemies building secret forts and supply deports in your zones 😉 ) Another possible bonus could be a steady stream of money from each gatehouse/zone.
As an addition to the idea, each faction could use a coloured block of wool for their flag, and uses those blocks (in a high visible place) to show who owns what gatehouse/fort. If another faction can steal the opposing factions flag and replace it with theirs, then they can lay claim to that gatehouse/fort.