First, there are some problems in the current WvWvW system.
(1) Priority goes to EB. Why? Because there is a castle to fight for. This makes EB queue almost a queue impossible when the 3 borderlands are accepting participants.
(2) All the 3 borderlands look the same. It does not really matter much which one you join. Just 3 identical battlegrounds with the exception of minor difference in the one with your world’s name.
(3) Possibility of World Alliances to corrupt the whole system. You don(t know if it really exists. It would be very hard to prove it if it really exists or might in the future. But if it is theoretically possible, the system needs a safe-guard. And it is reasonable for 2 worlds to do that to obtain a win-win relation while the 3rd world suffers and results in players abandoning WvWvW. Imagine players have to abandon WvWvW because they think there is an unfair world alliance, even if it does not actually exists. They might never come back after a week.
(4) In an A vs B vs C battle, sometimes prejudice can change a lot of things. Suppose World C is in fact as good as World A and World B. However, if both World A and World B thinks that World C is inferior, they would both focus on attacking World C, resulting in a 2 vs 1 battle even if there are no commitment between A and B.
My suggestion is to minimize the work needed for the changes while providing solution to existing possible problems.
(A) EB would remain the same.
The 3 borderlands would be:
West Borderland: World A vs World B
East Borderland: World A vs World C
North Borderland: World B vs World C
Players of World A cannot enter North Borderland to intervene.
(B) Player limit for borderland would be 1.5 times since there are only 2 worlds in each of them.
© The north part (where the home world suppose to be) of the borderland map would become something like SM. It will be best if we can add some sort of PvE mechanics here, like adding 3 bosses guarding 3 gates, and players have to kill the bosses and claims all 3 gates in order to take it, because there are only 2 worlds here.
(D) The total scores of each borderland is only a bit less than EB. Now since EB and these 3 borderlands have different stories, they should have equal priorities in a player’s choice. So you will have something like 3xEB now.
(E) It will be hard for World Alliance because you have to fight each other without the 3rd world. You will also have to face an enemy alone in a specific borderland.
(F) Even if any world alliance exists, it only affect at most 50% of the WvWvW now.
(G) If there is an extremely powerful world, they can’t take 99%. Instead they can only take at most 75% of the whole map. The 2 remaining worlds can still have fun in their own 1vs1 borderland without the interference from that super power.