All righty, here's one. I'm not sure how controversial this is, but usually I don't hear people talking about this at all, and when they do, they don't seem to complain.
I really dislike pretty much every song transition on Octavarium. The songs themselves, as compositions, for the most part I love. Even the Answer Lies Within, which doesn't seem to get a lot of love, is one of my favorite of their piano-driven ballads.
But this thing they did where the songs transition into each other feels to me like a waste of time to me at best, and an annoyance at the worst. I know, the whole album is filled with all sorts of nuggets, and that those transitions are supposed to represent the black keys on the piano or whatever, but my appreciation for nuggets doesn't supersede my desire to listen to music without long, boring intros and outros, especially ones that bleed right into the musical parts of the songs, such as the intro to I Walk Beside You. And don't even get me started on the intro to Sacrificed Sons.
So yeah, after ripping the CD, I edited the whole thing down to simply be a collection of songs that start and end concisely, without any overlong intros and outros.
The "Greatest Hit" versions of I Walk Beside You, Sacrificed Songs, and The Answer Lies Within were a godsend, since they omitted the chirping birds and ticking clock that overlaps with the introductions of the songs. And that's pretty much exclusively the way I listen to this album these days.