First, consider some of the great two-sided rivalries in MMOs: Horde vs. Alliance; AFS vs. the Bane; Humanity vs. Hell -- Mankind vs. the Cylons fits right in. In fact, since the show itself manages to portray both sides as sympathetic, there isn't too much storyline massaging to be done; the universe of Galactica is nicely morally ambiguous. All that really matters is survival.
Now, on the side of humanity, the one-to-one ratio between show and game is in plain sight; if you chose to play a pilot, you'd get to choose your character's name and callsign, and start off as a 'nugget' -- BSG's version of 'noob'. Nor would you necessarily need to limit yourself to that post. Any self-respecting Battlestar needs a full complement of personnel to function, from engineers to marines to communications officers, and all roles between. However, it needn't stop there.
There are two groups of humanity on BSG: military, and civilian. There is an opportunity here to play the role of crafter, making supplies for the fleet, whether it be refined ores, food, or medicine. No shortage of service-oriented jobs exist, as well -- mechanic, waste management, information tech. Though it's glossed over in the show, there is probably an ad hoc police organization patrolling the rag-tag, fugitive fleet, and that might be fun to play as well.
And where there is law, there are criminals -- playing the seedy underside of humanity can be just as fun as its champions. Consider working the Black Market, supplying badly-needed drugs to those farther out in the fleet, frequently overlooked by those in charge. Or perhaps you'd prefer to play as muscle, either shaking down local markets as part of a 'protection' racket, or being security for a popular club.
On the Cylon side of things, however, it gets a little harder to make compelling and diverse roles. There are three basic models on the show: the human-looking type, each given a model number; the Centurions -- the large, non-speaking, metallic warriors; and the Raiders -- fighter ships with Cylon brains embedded in them, partly organic. Aside from the 12 humanoid models, with their unique and specific appearances, and the other models, each one looking just like the other, it would be difficult to enjoy any sort of customization of character. And who would want to be known as 'Number Four' -- or, more likely, 'Number Four-Thousand, Nine-Hundred, Seventy-Three'?
We'll have to take some liberties with the license, then. Let's say that this MMO takes place after the events of the show -- during a time of armistice (which, incidentally, is how the show first begins, after a period of truce). Let's say that the two sides have agreed to try to live peaceably with each other, and pursue their own destinies, in their own corners of the universe -- for a time, that is. Such a peace cannot, of course, last for long, so the setting could be a period during which small skirmishes in the DMZ were fought, a possible prelude to a new war between the two civilizations. Gathering intel, the human military discovers that the Cylon race has now developed fully autonomous, unique humanoid units, each as individual as humanity itself.
Further information gathering (by a possible Spy subclass) reveals that Cylon brains are now transferrable between host bodies and various fighting units, such as the tougher, armored Centurions, and the space-capable heavy craft of the Raiders. Thus, a player who wanted to play as a Cylon would now have as many opportunities as one playing a human.
This is not to say that the humans have been idle; having been caught by surprise and their very race threatened with extinction as a result, the military has built a fleet of new Battlestars, with upgraded weapons and armor stats, and developed new, smaller and more versatile ship-to-ship fighters as well. The ability to both ambulate on the planet's surface and fly a fighter into space would be a huge selling point for this MMO.
What would the goal of all this frenetic activity be? As per Tabula Rasa, there might be ground to be gained -- hotly-contested areas of strategically-important space; resource-rich asteroids and planets. Control of shipping lanes would be important. Sabotage missions that rely on stealth and speed. In the non-military aspect, there are new technologies to develop, repositories of historical records and scientific information to preserve and defend, vast accumulations of food and raw materiel to safeguard.
From a gameplay standpoint, how would death mechanics operate? The Cylon side already have cloning and resurrection technology; we could assume that those secrets have already been stolen and duplicated for humanity, tailored to fit human biology more precisely. Is there a place, or need for the grind? For military purposes, 'leveling up' comes in the form of rank status elevation, or promotions. These could be based on number of confirmed enemy kills, a given number of which are necessary for advancement.
But in the civilian corps, there might not be any need for advancement. Perhaps this could be treated in a Sims-like fashion, where researching a new skill and developing it take the place of levels and skill points. If you want to learn something new, access the online courseware and spend some time learning a new skill the old-fashioned way. One could even enter the military with advanced knowledge of a subject, and start off at a higher level than a completely new recruit. In fact, this game needn't be entirely about fighting the war all the time; you could try your hand at living a normal life, and choose to support the war effort a quieter way.
We can already see the expansion: Galactica Classic, where you travel back to the future, to the brown and beige uniforms of the Battlestar Ponderosa. Fight with lasers instead of projectiles! Interact with latex-y looking alien races! Cringe at the sight of freaky robot-dogs! And marvel at how hard it is to aim as a Cylon with only a single, wandering eye to contend with.
To summarize, BSG is a great candidate for an MMO, and considering that the show is in its final season, we geeks are going to need something to fill the void -- and that spinoff just ain't gonna do it.