This sounds really good, but I was thinking that you would choose a background, and the main quest (or at least the intro) would be based on the background. For instance, if you chose the Royalist faction, you could start off as a noble coming back to his estate when he hears news that his family was slaughtered and his home was burned down. But also, just so you wouldn't be limited, you would be able to switch sides a few quests in. So, once the Royalist hears his family was killed, he goes London for the king's help. The king would then refuse him, and he would have the option to join the army. On the other hand, you could get mad at Charles for not giving help. You would then find out that it was actually King Charle's men who killed your family so he could acquire your property, and you would join the rebels.
If you chose to start out as a rebel, you could start in a royalist prison because you were in debt. The prison would then be stormed by other rebels, you would be freed, and you could join the Parliamentarist faction. Or there would be some quest where the royalists ask you to infiltrate the rebels, in return for property and money.
If you choose to start as a French Mercenary (if there is that option), you would come into England on a ship. You would then do a couple quests for each side for some pay. After the the few quests are finished, you could choose to join the Royalists because they pay more, or the rebels because you feel sympathy for them.
But, like Kroot says, this may seem too forceful an intro. I know for me even Oblivion's intro was too forced (there was no way a noncriminal character could not deliver the amulet from a roleplayer's perspective).