Souls in the Great Machine should be thought of an "over-stuffed" book, like an over-stuffed burrito or something. It's got so many plot threads and characters you really need to be taking notes to keep it all straight, and it dives right in without a lot of introduction.
This is both its strength and its weakness. There's a lot of interesting things to read, and the density and variety make it pretty compelling. But it seems like McMullen wasn't really able to keep good control over all the bits and pieces, and some plot threads appear almost out of nowhere, late in the book, without any setup. It actually turns out they're setup for a sequel, but they're still jarring.
Also jarring is what seems like rather abrupt personality shifts in some of the main characters. Some characters are reasonably well-developed and feel very real, while some feel like they're just taking a certain course of action because the author needed them too.
Having read the sequel (more on that later), I can say he gets better at dealing with this, but there are parts in Souls of the Great Machine where I just though "why would she do that?"
It's worth a read, just for the sheer invention of the whole thing, and judging by the sequel, he seems to have improved his technical handling of this style of writing. There's a third book in the series that I'll be reading soon, and I'm hoping that he continues improving as a writer in that one.