I was thinking some more on some of the missions, and the discontinunities that are comming up with the Featured Episodes. My proposal:

The following missions/fronts are active at start. Multiple active fronts should occur concurently:
All cluster exploration missions for all areas
All Defend Sector missions (kind of hard to do for Romulan and Cardassian Sectors, but activate them none the less)
Klingon/Federation war missions (Klingon Front for Fed, Klingon Sector for KDF)
Deferi/Breen Featured Episodes
Romulan Front missions starting with "Under the Cover of Night". Reman Featured Episodes should start after completetion of "Minefield".
Cardassian Front missions.

The Devidian missions should become active after completion of both "Under the Cover of Night" and "Suspect". Those two missions should be chained such that one becomes active after the other.
Again, "Cloaked Intentions" Reman Featured Episodes should start after "Minefield". Both of these sotry arcs should become active almost immediatly for the KDF(Lt. 7 or lower).

The Borg missions should start as soon as a player reaches Captain level 1. THis should be the same for both factions(make ALL Borg front missions open to the KDF). The Undine should start at BG/RA 1. The Dominion Featured Episodes should start after the player completes ANY one Borg or Undine Front Mission.