OK, seriously.  It's been a year since I read it.  And I have trouble remembering names at the best of times.  That said, when I read it, I was never confused by who was who.  But if you were, then I can understand why you might be confused as to the plot, because knowing who is who and who is doing what is important.  Heck, I only finished Prospero Burns a few weeks back and I couldn't tell you the main character's name anymore!   Though the plot is fresh in my head.

Me?  I'm used to reading Asian stories and histories with hundreds of characters/people (Three Kingdoms, Outlaws of the Marsh, Genji, Jin Yong Wuxia novels, Secret History of the Mongols, etc) so Mechanicum didn't even come close to a 'name on a page' level for me.  I've learned how to keep track of people in a book who are important while I'm reading it and that's that (Though as a funny related digression, I now find Asian names easier to keep track of than Western ones.  A complete polar opposite of most westerners :p ).  The best answers I can give for mains were the Female Tech Priest whose forge was being destroyed near the end.  The Knight was a sort of minor protagonist.  And I vaguely recall at least one other, probably something to do with Noosphere as well.

To me it was mostly a cool little, by the numbers romp.  Nothing terribly surprising.  The whole Mechanicum level of stuff.  Yeah, there were some odd sidestories like the things with Dorn on Terra that didn't seem to fit in very much, despite being cool.  But in those cases they remained important to the Series Narrative as a whole instead of the book as a standalone, revealing info on the mindsets of key players in the Crusade.  Heck, that's one of my more memorable lines in how it hinted that if he wanted, Dorn could have called back the two lost Legions...  But even in the face of Horus that was unthinkable.  (How weird is that?  Because it implies at least at this point they were still out there in some form...  Though admittedly later things hint they were destroyed too.  Half makes me think of a vault in Terra or similar with 2 Primarchs and their legions in Stasis...  But I digress)

As for the faith 'war' so to say, again, it's been a year.  But as I recall a key point was the dilemma of it.  And the discovery of the Void Dragon helping to call into question the faith of even the Loyalists, but them choosing to remain loyal despite that for whatever reason rather than reveal the truth to the traitors.

Graham may be a good writer but he lost lost of his old flavor in his latest books. Same Problem with Dan Abnett.

If i could pick a writer it would be Aaron Dembski-Bowden or Anthony Reynolds. Both draw a in their recent Books a fantastic picture of Chaos Marines "Society".

The Noosphere is the (as ever Abnett, Blessed be his Name, created - or ported if you prefer) explanation for the method of networked connectivity between members of the later Mechanicus (of the 40K era) that allows it's members to communicate at an extra-verbal level.  This has been implied before, but Abnett, Beloved by All, spelled it out in Titanicus, which is a fantastic 40K novel for all those heretics who doubt the divinity of Our Lord Wordmeister. 

Vendettar said:

People are always ready to claim Abnett's 'later stuff' is rubbish. Well ... I personally think the latest two Gaunt's Ghosts books are far and away the best two books of that series, especially the latest, Blood Pact ... which gives the hands down -no question- most interesting Chaotic-eye view of Archenemy soldiers in the canon. 

ADB is ... okay. He's getting better certainly, his Night Lord books are better than that zombie one he started out with, and his HH novel was better than his Night Lord books ... but he's still pretty green imo. I agree Reynolds is good, but I've yet to see much variety, they need to get him to branch out a bit.