Another idea that just came to mind, and which might even be a relatively simple change:
when the other faction controls the fort,why not also include a Cerano Medal as part of the reward?
This would make it easier for the Elyos to keep up with the Asmodians. As things stand now, if the Asmodians continue to receive two to three times as many medals per day, the imbalance in PvP instances will grow to a point where it is no longer enjoyable for either side. In the medium term, this will lead to more players quitting the game, simply because there is no longer any meaningful or viable PvP activity available.