I'm sure I'm going to get some flak for this but here goes.
There should be enough Patrol and Storyline missions in each sector so that a player can choose a particular front, be it Klingon(or Federation for the KDF); Romulan; Cardassian; Breen; or Borg and stick with it for their character's entire progression. There could also be a homefront as well.
The Homefront would be a mix of threats that must be stopped on the core worlds of Vulcan, Andoria, Earth, Betazed, Sauria, and the like. It could also pit the players against internal threats such as section 31, rouge Starfleet, Federation based terrorist groups (such as the New Essentailists movement), or just plain rowdy citizens.
The Romulan Front could involve more characters such as Commaner Rashka (Obisek's 2nd in command), Taris and her Reman lackies (The Reman commanders at both Iconia and Hobrus), Commaner Jarek (the Tal Shiar officer that died a "mysterious and inconclusive" death at Hilfar), Ambassador Tomalak, Admiral Tebok, and others.
The Cardassian Front low level missions could involve Former Bajoran Milita officers in Starfleet that have not entirely gotten over the occupation, and issues with Bajoran-Cardassian relations.
I do like the concept. I thought about something similar. What could be done is that Starfleet Command issues you orders to a certain sector block lets say maybe a week or so and what happens is that while you are under those orders you gain double the XP and merits for missions you complete in that sector. Granted it would only work for leveling but it's the best I can come up with.
While what you're asking for certainly makes sense, realize that you are asking for is the equivalent of six different factions, all with content from 1-50. You're just not separating the "fronts" among different factions or prohibiting the same character from choosing multiple fronts.
Right now the devs do not have PvE content for the Klingons from 1-50. They barely had time to come out with content for one faction from 1-40. And I don't know of any MMO ever released that has had more than one full content path from 1 to max level for a single faction. (I would say as a wild guess probably about three to five factions with full content is the limit)
This game's setup has been pretty standard for MMOs. One front, in a different zone, for each of 10 levels along the way. So there is the 1-10 front (the Federation proper) the 11-20 front (Klingons) 21-30 (Romulan) 31-40 (Cardassian) and 41-50. (Borg)