OK I've come up with a faction list, all would be playable, tell me what you think:

The Parliamentarians

The "roundheads" with their NEW MODEL ARMY, they'd control most of the south (the richest lands) and parts of scotland.

The Royalists

The "cavaliers" raising their armies from the supporting Lords and land-owners, they'd control the north, wales, cornwall and ulster.

Scotish Rebels

Raised from the clans opposed to the English after their attempt to impose Anglicanism on the Scottish. They'd control lands not loyal to parliament or the royals. (I'm not to sure on my scottish history, maybe someone could fill me in on some details?)

Irish Rebels

Raised from the Irish or southern Ireland who were opposed to English rule. They'd controll all the provinces in Ireland except Ulster who were mainly English and so still loyal to the crown.

Thrashaholic