A new idea for the FE would have a FED only and a KDF only set of stories. Each one will tell a different story and focus on the main STO story line concept UFP vs KDF war. The UFP story will show the end and the KDF can show the beginning. Since every KDF player has a FED character, and a lot of FED players does have a KDF character, and it might even kick off more creation of KDF characters.
Then after those two FEs, start doing FEs for each of the campaigns in the story lines to help finish them and then finally, do original stories.
Secondly, I think that the Battle of Vega tutorial would be better suited as the first mission to introduce the Borg story line and have a UFP-KDF battle to replace it. This new tutorial can be a mirror one to the KDF to either fighting the Feds or another enemy.
Third Concept, take the Traelus-Alhena-Sh'mar-and Salvage dailies and put them into Beta Ursae where it makes sense to have the True Way show up. Naturally, rename the systems.
Fourth Concept, rework Ker'rat to be a UFP-KDF battle rather than a Borg one. Then have the Borg war zone in Gamma Orionis.