His comments about the dearth of talent/originality is squarely aimed at Marvel/DC and superhero comics. He's spoken of non-mainstream comics a couple of times, most recently Craig Thompson.
Yes, but in that interview he states that he doesn't read comics anymore, so it's understandable why the reader might form the impression that he doesn't read comics anymore, and thus that his view of current comics might be somewhat restricted.
I do always read that as he doesn't read comics from The Big Two, just cos' I've seen pull quotes from him on a couple of non-mainstream books over the years but yeah, it's is a fair point that he's seemingly contradictory. Even if it is a contradiction or he's not clarifying every thing he says, I do think a lot of people are focusing on this small point of his and using it to dismiss everything else. Maybe he figures if it WAS that good, it'd be selling incredibly well and he'd be hearing about it in other areas rather than just comicdom. In which case, he has a point

Some US creators are taking it really personally yet their reaction makes it clear Moore still carries a lot of weight in comic book circles.
I didn't read your initial comment as dismissive either by the way and I'm 100% in agreement with you on your last point. What's even sadder is how it's driven such a wedge between Moore and numerous friendships (and yes, I do think his paranoia/bad blood got the better of him there. I get the impression he thinks this too maybe, he mentions it a few times)
I thought his little insights into how DC editorial is operating is interesting: the idea that the New 52 was pushed forward cos' they were worried about the legality of Before Watchmen. That does mesh with reality: New 52 was very rushed while it seems the work on the Watchmen prequels has been done and dusted for a surprisingly long time now. Also it appears to me that he seems to be more specifically talking about Brian Azzarello than anyone else; he does mention at one point that he liked Azzarello's Constantine run with Richard Corben and provided a "fulsome" pull quote for the collected edition (and deservedly so, it's a great story!) He mentions the Rorschach comic specifically and there's a few other lines in there too that suggest he's more hurt by his inclusion than some of the others.
The whole thing just points to how fucked-up the thinking of the Big Two really is. We could be living in a world where Alan Moore was still happily making comics. Maybe that could be one of their 52 bloody universes, eh?!