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.
I pity you that you dont enjoy Hex Omega, I love the outro, it reminds me of face of melinda (tapes verision in particular) and deliverance. Know that I do respect your dislike for it, especially since you motivated it. Personally I think the church organ usage was perfect, it wasn't some over-ambitious thing (big chance opeth would do that, heh. :SARCASM
Overall the church organ usage didnt play a big part, it just melted in perfectly, imo, and I think a lot of people that listen to hex omega really enjoys it even if they have no idea there is a church organ used in the outro.
Also you mention isolation years, which I wholeheartely agree with you being a perfect closer to ghost reveries. But you mention the sort of "conclusive" feeling it gives you, well, this is exactly what I felt about the hex omega outro since they play the same note through the outro and then in finishing with the church organ alone. I think it couldn't be more period that that.