You are definitely not alone, I agree.
In reguards to Hex Omega, it is as fragmented and incoherent as Mikael has ever written. Don't get me wrong, it does quite follow the "intro-verse 1-chorus-verse 2-chorus-interlude-outro" structure, but there are few transitions (and even fewer that work). It seems like a conglomerate of riffs put together. In addition, I don't feel it really GOES anywhere. What emotion am I supposed to feel? Anger? Sadness? Rage? Desolation? Not really feeling anything...
Oh, and the outro riff, IMO, is horrible--probably the worst way (IMO) that any Opeth album has ever closed. First of all, there is scarsely a transition into it...it just happens. Second, it's ugly, slow-moving, and quite frankly anti-climatic. Really doesn't fit the song at all. Not a fan.
Isolation Years...now THAT was a closer. Not that all Opeth albums have to end on a soft note, but something that really leaves you with a feeling of conclusion or sadness or loss. Hex Omega really doesn't do that for me. Oh, and the organ use was soooooooooooooooooooooooo overhyped! Wow, one-long, drawn-out chord...good job. I wanted to hear a super evil riff that was truly capable of destroying a church organ.
Meh.