Agreed so, so much. YOTBR is to Coheed what The Resistance is to Muse. It's really a fairly great album, but fans love to hate it to prove how "hardcore" they are. I view it as the album where Coheed embraces their metal side, and Afterman the album where they embrace their progginess.
"The Afterman" might be their least progressive record to date. Not really sure where you got that from... All of the songs are fairly non-adventurous and short, besides "Domino." There's nothing progressive about "The Afterman," "Mothers of Men," "Goodnight Fair Lady," "Holly Wood" "Vic The Butcher" and "Subtraction," and that's like 90% of the record. That obviously isn't a knock on the album though. I loved "Ascension" and I can't wait to "Descension." Maybe the notion of releasing a double album is progressive, but both parts of "The Afterman" are essentially just as long as "Good Apollo 1." Speaking of; their most progressive influenced record would hands down be "Good Apollo 1."