Aha, that does sound like it could be an interesting approach. And Paine is such that you could probably change some aspects of where he was without causing too many people to shrug, considering his somewhat lesser role in the realm of American History relative to the other founding fathers.
His lesser role, as in, the lack of attention he gets; or, his lesser role, as in, an objective contributor to the Revolution? Don't buy the hype, man. His fucking face should be on Mt. Rushmore and on our currency and in all our textbooks. He may have never held major office or led troops on the battlefield, but he was a master strategist in his own right.
I am totally impartial. Absolutely no bias, whatsoever. Yup. None.
Edit: The blurbs in the OP are solid, but there is much you can add for Paine. During his stay in France, he was able to procure millions of dollars in grants and loans from the French government to aid the American cause. In fact, he had an ardent fan base in France as he was a fervent supporter of the French Revolution. There are even stories of Paine's encounters with Napoleon; friends at first, Paine was quick to condemn Bonaparte's actions soon after. Most people reference Common Sense a polarizing agent in the war, however, CS was much more than that. It marked a shift in political discourse that could be considered uniquely American at the time: it made the positions of the average person worthy of consideration. It was written by an elite for the non-elite. It alluded to the Bible over lesser known works of Latin -- it was just brilliant. Not to mention the less impactful but equally as profound Age of Reason and Rights of Man. You don't realize how many decades ahead of the curve Paine's thinking was until you read The Age of Reason. All this compounded with how he was treated upon death and his notoriety -- or lack thereof -- in contemporary political discourse leads me to champion his name as often as I can.
Bleh.
I'm tired and frustrated. My rambling is probably a poor combination of actual history, Wikipedia, jingoism, and pizza. Whoever ends up doing the OP (iNvidious01 is not perma'd, right?) needs to make it a collaborative effort. I think a history refresher course to supplement the OP would be brilliant. Like, the Jefferson thing in the OP, I was unaware that he was so far removed from all the action. Nevertheless, Ubisoft needs to have him in there. As much as it would kill me to not see Paine get some recognition, not having Jefferson be a major player would be absolutely ridiculous. This is ultimately a work of fiction and should function as such. Smudge the history all you want Ubisoft: I'll take Jefferson railing the Queen and not returning her letters than no Jefferson at all.