Gendo's already despicable as it is, so it didn't shock me that much that he ate Adam. Shinji realizes the one truth that has been hovering around him for some time now, that all of his friends, all his loved ones are separated from him in one way or another. Kaworu seems to have some doubts regarding the motives of SEELE.
As for SEELE, quite frankly the worst part of Eva imho. They sound like a pathetic cult. I was hoping the manga would manage to gape this massive flaw that was present in the anime, but oh well.