Most of the ideas regarding the winning alliance and the post fortress game, involves a huge game play change, technically meaning a brand new game, and I think we can all agree on that that will never happen.
However, there is one way that is effective and and also require "minimal" game changes: Every player that have been involved in destroying of the Fortress, gets his privilege to recive POI bonus revoked for a period of, say, one month. This will dramatically reduce the power of the winning players, thus giving the competitive alliances a big chance to catch up and claim the center.