Red haired Cavaliers, Neanderthal Roundheads: Ben Jeapes, New World Order, (London: David Fickling Books, 2005)
I have just finished reading Ben Jeapes's YA novel, The New World Order, in which aliens descended from neanderthals (who long ago emigrated into a parallel world) return to invade England three years into the English Civil War.
Charles I and James get killed by an arial bombardment, Charles II marries his sister off to the half-breed son of the alien general to make peace at the end--but with uncomfortable historical glitches such as Charles II introducing actresses to England. I wonder if he would have done if he hadn't spent time in Europe where it was normal.
Cromwell ends up leading God's Army, a guerrilla force attacking both aliens and Royalists. Fairfax is in exile but brought back by Charles II to lead the armies against the aliens, and Monk works for Charles II but this time sends letters to Cromwell on the sly.
The aliens are pagans who can use the ley lines, and want toevangelise the English (as well as conqering and settling). They crucify people to prove the untruth of the gospels. One of their first victims is Matthew Hopkins who, it turns out, really can smell witchery.
The characterisation isn't wonderful: this is Cromwell as cardboard Puritan, which he never was, but it is rather fun. Because Neanderthals can breed with humans but not as a matter of course, atthe end of the book the Holekhor are left stranded in England knowing that they will be a thin strand in the nation's blood.
What is less clear is what the impact of foreign technology will be--will there be learning or will the advances the Holekhor have brought with them simply disappear. How will the European powers react to an England which now has better weaponry than they do (we already ready know they have fortified their coasts). Charles II has not married Catherine of Braganza so there may be a legitimate heir to the throne. With James II dead already, there goes the Stuart disaster, and of course there will be no King Billy (Cromwell hasn't taken Ireland either). I think Jeapes is Catholic so you could regard this as a counter-reformation alternate history, even if England stays Protestant.
Jeapes does a pretty good job of creating the political difference of his world, but ironically for an sf writer falls down on the world building. Almost any historical novelist could produce a more convincing seventeenth century than this. What I suspect happened is that Jeapes forgot that the past is an alien planet.