Here's an opinion of mine, which I think is a bit controversial, that I thought of while listening to Black Clouds & Silver Linings again, inspired by the recent thread about that album:
The Shattered Fortress is what the band intended it to be: a well-structured finale to the Twelve-Step Suite that calls back to the other songs while existing as its own original musical entity, NOT a poorly made mish-mash of riffs. It's also one of the best songs in the suite. They fluctuate in my esteem (for example, I was really hot on The Glass Prison and The Root of All Evil and cold on This Dying Soul and Repentance for a while, now it's basically flipped), but The Shattered Fortress is the only one that I consistently love without qualms and has never been outside of my top 3 in the suite (currently: TDS, TSF, TGP, Repentance, TROAE).