I agree with Moonlapse about The Twilight Is My Robe. I like the riff that comes right after the solo, but it does ruin the build-up. Then again, Mike always said that his songs are adventures. The songs often go lots of places. I think the solo represents a short lived moment of triumph, then it slows down again.
I don't see what could've been done with the end of The Night And The Silent Water. Where would it have gone from there? It was the perfect build-up, but I have trouble "picturing" what might've come next. I don't have the album here at my dad's, so I'm not sure if this is actually done in the song, but... I think that they should've faded those two guitar chords at the end of the song in, and it should mount, getting louder and louder, until it's ended on one, powerful electric guitar chord.
How could anyone not like the ending of White Cluster?! That used to be my favorite moment in all of Opeth's music. I love how the song fades out on a lead... And that beautiful, gentle guitar part that comes several seconds later.
I love the piano at the end of The Leper Affinity, I just think there was a bit too much. I think they ended it on an odd chord. I think they intended to do that, just so you'd be taken by surprise, but I really wanted a solid ending.