Broken Base - Morrison is one of the most polarizing authors in comics to date.
In particular, his New X-Men run is polarizing even amongst ardent fans.
Complete Monster - See Card-Carrying Villain above, then add to that a level of depravity and malice that seems to exist only to perpetuate evil. Be it the brain-washing academy in the The Invisibles, Cassandra Nova's entire campaign during New X-Men or the full despair of a Darkseid-run Earth in Final Crisis, Morrison loves to set his protagonists against pure embodiments of evil and submission.
Mary Sue - Deconstructed with Damian Wayne, as many people (including Bruce, his father) think he's an annoying little snit. It's a matter of personal opinion how successful this deconstruction is, since many readers argue that he nevertheless embodies certain Sue-ish qualities played entirely straight.
There's also the fact that in Batman #666 we see a grown up Damian who suspiciously looks a lot like Grant when he takes his mask off. This was actually Kubert's design idea, but it wasn't the first time something like that had happened.
Squick - One of the characters in The Filth is a porn actor with... unconventional fluids. The New Gods' possessing of characters in Final Crisis (Mary Marvel possessed by Dessad, Dan Turpin's... "death" by Darkseid's taking over his mind).
Villain Sue - his JLA villain Prometheus is an excellent aversion of this trope, pretty much encapsulating how to make a Badass Normal a Justice League level threat without dipping into God Mode Sue levels of Crazy Prepared. While Prometheus does some incredibly Sue-ish things - notably curb stompingBatmanoff panel - he also has crippling psychological flaws, oversights in his planning, and a few kinks in his advanced technology. Essentially, he spends one issue in Villain Sue territory before the sheer magnitude of his undertaking comes crashing down around him.