This was a thought-provoking post but I'm not sure I would agree with all of what you say about Adamson's work here. (You will probably have guessed that having read my own review of the book!). I think it's a bit unfair to say it's light on analysis: the sustained way in which Adamson unpicks the factional manoeuvrings behind the Junto, and particularly the complicated Anglo-Scottish-Irish connections, are to my mind highly analytical and considered.
And he does devote lots of space, too, to understanding why a certain section of peers and MPs were so hostile to Charles I's policies during the Personal Rule. he does not arrive at a class-based explanation of this group's actions, but on the evidence I think he's right to locate their opposition in political and religious ideologies: or to put it another way, to prioritise superstructure rather than base.
Perhaps it's fairer to say that Adamson's book does not really engage with those below the level of the political class. There are moments when he takes a rather monolithic view of politicians controlling the London crowd: it was probably more complicated than this, and while some protests in 1641 were I'm sure engineered or at least tacitly supported by the Junto grandees, many more will have owed their origins to the indepenent political agency of those participating in them. But to carry out a sustained analysis of the vertical links between politicians and "people" would be a very different work of history, and add hundreds of pages to what is already a monster of a book.
And the book does stop in January 1642, which means that its chronological scope can't really cover some of the things you mention in your review. Within these limits I think it is absolutely reasonable for Adamson to argue that the outbreak of the war - in the sense of Charles and Parliament coming to blows - is driven by the sustained efforts of the Junto to achieve a quasi-republican settlement. Yes of course when it comes to recruiting armies, to choosing sides etc this doesn't look at the motivations of working people, but in terms of Adamson's focus - what was going on in London/Edinburgh/Dublin politics that caused the rift between King and Parliament - the book, for me, breaks new ground.
I'm sure you're right that Adamson has some sympathies with Charles I (and Strafford, too) - read his chapter in Niall Ferguson's "Virtual History" for a rollicking attempt to imagine the ancien regime in England continuing into the late eighteenth century had Charles only been able to defeat the Scots. But I'm not sure you can argue that he denigrates Cromwell because of his politics. See for example his chapter in John Morrill's "Oliver Cromwell and the Puritan Revolution", in which he conducts a close and considered analysis of Cromwell's attitudes to Parliament and his behaviour in the Long Parliament.