Who would you have supported in the English Civil War?

[Wikipedia delenda est]

Apologies for the excessive quoting, but Theodore Roosevelt just writes so well on what a tragedy the Restoration was:

The King and his followers then took revenge on the dead body of the man whose living eyes they had never dared to face. The bones of Cromwell, of his mother, and of Ireton, were disinterred and thrown into a lime-pit; and the head of the great Protector was placed on a pole over Westminster Hall, there to stand for twenty years.

The skull of the mighty crown-grasper, before whose untamable soul they had shuddered in terror, was now set on high as a target for the jeering mockery of all who sang the praises of the line of libertines and bigots to whom the English throne had been restored. For twenty-eight shameful years the Restoration lasted; years of misgovernment and persecution at home, of weakness abroad, of oppression of the weak, and obsequious servility to the strong; years when the Court of England-devoid of one spark of true greatness of any kind-was a scene of tawdry and obscene frivolity. Then, once again, the principles for which, in the last analysis, Cromwell and the Puritans stood, triumphed; the Dutch stadtholder came over the narrow seas to ascend the throne of England; and once more the current of her national life set toward political, intellectual, and religious liberty.

Also, another quote to build on CrabCake's point:

Oliver surely strove to live up to his lights as he saw them. He never acted in levity, or from mere motives of personal aggrandizement, and he saw, with sad, piercing eyes, the dangers that rolled around the path he had chosen. He acted as he did because he conscientiously felt that only thus could he meet the needs of the nation. He said to the second Protectorate Parliament: "I am a man standing in the place I am in; which place I undertook, not so much out of hope of doing any good, as out of a desire to prevent mischief and evil--which I did see was imminent on the nation (for we were running along into confusion and disorder, and would have necessarily run into blood)."

We are often told that the best of all possible governments would be a benevolent despotism. Oliver's failure is a sufficient commentary upon this dictum of the parlor doctrinaires. There never has been, and probably never will be, another despotism where the despot so sincerely strove to do, for a people capable of some measure of freedom, better than they themselves would have done with that freedom. The truth is, that a strong nation can only be saved by itself, and not by a strong man, though it can be greatly aided and guided by a strong man.

Slightly off topic here, but while I am partial to the consideration of William III as a reasonable revival of the Protectorate in some ways, it gets into some problematic territory. Especially when you consider the fact that William's mother was a daughter of Charles I and his wife was a granddaughter thereof as well and this is the origin of both of their claims to the throne. Furthermore, the dynamics of the Orangist faction in the Netherlands relative to their opponents makes any such allegories between William III and the Protectorate problematic as well, especially seeing as how the 1650s were bad times for both the Stuart and Orange families, as the "royalist" or "more royalist" faction in an "anti-Royalist" period in both countries. Lastly, it must be remembered that while William III did in fact sign off on Parliamentary authority to determine the King and the declaration of rights, these aren't necessarily reflections of his personal views. His priority and and interest was securing England as an ally against France and taking the English throne helped to ensure that, and the concessions made to achieve that were secondary concerns to him.

What I think the Glorious Revolution represents, was the confluence of events and interests aligning to allow for the successful melding of the two opposed political traditions of Monarchy and Liberty into a combination that would endure for centuries, albeit with the former being steadily eroded over time. There are some similarities with how the Orleanists tried to meld the French Monarchy with the Revolutionary traditions and had conditions been more favorable and the timing been better, it might have worked.

I do agree with Roosevelt about Cromwell being of higher character than Napoleon, at least in the time period referenced as such.

Actually, there's a paragraph right in between the two quotations I provided (I left it out due to length) in which Roosevelt goes on to qualify his comparison of the Protectorate and the Glorious Revolution, and his preference between the two is clear. According to T.R., "Cromwell and the Puritans had gone too far", while "the men of the second Revolution had learned the moderation which the men of the first had lacked....They possessed the inestimable advantages of common-sense, of moderation, of readiness to accept compromise." Having read Steven Pincus, I disagree with this interpretation of 1688 as a consensual affair, but that's another topic entirely. It is undoubtedly true, though, that the Revolutionary settlement of that year was far less radical than the one 40 years before.

Regarding your points about William III vs. the Protectorate, I agree completely. In fact, I would go a step further: not only were the Stuarts and Orangists both down on their luck in the 1650s and not only were they dynastically linked; they were also close allies in a period of ideological and military warfare between republicanism and monarchy. In Pincus's first book, Protestantism and Patriotism, he dispels the notion that the first two Anglo-Dutch Wars were fought over trade. Instead, they were fought between republicans and monarchists in England and in the Netherlands, with religion as a contributing factor. The first war occurred just after the beginning of the Stadtholderless period, but Orangists remained strong and still formed a sizeable part of the Dutch political nation. As Pincus shows, it was Orangists who pushed for war with England against the wishes of the States Party, and in England the war was portrayed as a battle against monarchical Orangist and Stuart elements rather than the nominally republican Dutch. This ideological rather than economic explanation of the war is further proved by the English insistence on inserting the Act of Seclusion into the peace treaty, which was desired both by Cromwell and de Witt. The second war was part of the same ideological conflict, only the governments of England and the Netherlands had switched places. In the intervening years between the first and second wars, England's monarchy was restored while de Witt and the republicans consolidated their control over the Dutch state. As Pincus shows, it was a clique of Anglican Royalists who pushed England to war with the Netherlands in order to punish their republican apostasy and advance the interests of the House of Orange. This was well-understood both by the Orangists, who treasonously intrigued with the English, and by Algernon Sidney, who proposed to de Witt a Dutch invasion of England to revive the Commonwealth. Pincus doesn't cover the third war, but that was also embarked upon by the English to support William of Orange, though they soon found him less pliable then they had imagined. Even so, he took the opportunity the English gave him and had the de Witt brothers brutally murdered and himself restored to the Stadholderate. It was this man, this enemy of Cromwell and destroyer of Dutch republicanism, who would go on to become Theodore Roosevelt's imagined savior of the Protectorate. Problematic territory indeed (keep an eye on For the Good Old Cause ).

Nevertheless, it is undeniably true that most radicals and former Cromwellians supported the Glorious Revolution fervently, which begs the question why. I have often been perplexed by how willingly they threw their lot in with William; it seems no less than a total betrayal of the Good Old Cause. But the reason, I think, is that after the Restoration the Overton window of English politics shifted considerably to the right. In the Commonwealth period the Dissenters were in power and divided amongst themselves, meaning the left was taken up by Independents, the center by Presbyterians, and the right by dissident Anglicans. There was no place for Catholics in this arrangement, though the more left factions often accused those to their right of being papists. After the Restoration, however, all Dissenters were persecuted alike and so were grouped together as Nonconformists. In this new alignment, Nonconformists comprised the left, Anglicans the center, and Catholics the right. Some may question my placement of Catholics on the right because of the discrimination they faced, but Catholics actually wielded considerable influence at the Restoration court through the Duke of York, influence which they used to promote absolutism and the re-Catholicization of England. This circle of Jesuits and Gallicans which James II surrounded himself with were the far-right of English politics, and however much the radicals may have disliked William of Orange (considering their first choice was literally a son of Charles II), he was the instantly preferable alternative. They weren't going to get a republic with William, but at least they might get a limited monarchy and guarantees of their liberties, rather than the arbitrary government and slavish tyranny which popery always entails.