Sounds like a great idea to me! If you ever need anyone to write flavor text (unit descriptions, building descriptions, traits, etc.) then I'm definitely willing and able to help (I've got loads of free time).
Plus the Jacobite uprising is a great time period to cover. I live pretty close to Derby, famous for being the furthest Bonnie Prince Charlie got before he turned his army around.
History might tell you it was because he was responding to the threat of a British army, but don't you believe it. It was really because he got to Derby and realised the whole campaign just wasn't worth it (Derby can have that affect on you if you travel there.)
Plus there can be more than two factions. There were several different clans in Scotland at the time that took different sides. You could even include the Dutch and maybe Ireland if you wanted to extend the scope a little. It would be interesting to see what would happen if other areas under English control jumped on the revolutionary bandwagaon.