The songs are just too damn bloated on BC&SL except Wither (which is perfect and one of the best DT ballads IMO). This is a common complaint of mine about post-SFAM MP-era DT...too much unnecessary padding to make very long songs for whatever reason. I don't think there's a single song over 10 minutes in this period that I don't feel like goes on too long. I can't say that about any pre-6DOIT or MM-era song.
-Nightmare could lose a solid 6 minutes and be a great song. Too much noodling and repetition after the Beautiful Agony section and the growling part is the dumbest thing this band has ever done.
-A Rite of Passage's solo section is mind-numbingly boring. Just endless key & guitar solos trading off. The main riff and chorus is cool but the entire middle section could be wiped out and you'd be left with a great 5 minute prog-metal song.
-Shattered Fortress is probably my favorite of the 12 Step songs but the intro lasts way too long. The rest of the parts feel like they last an appropriate length so this one doesn't bother me. This is not a suite by the way. It's just 5 songs that share a few themes. I dislike how it's been retconned into being viewed as one coherent epic.
-The Best Of Times. I get that the sentiment of the lyrics is really personal, but I just cannot get over how juvenile they are. Sometimes simpler is better when discussing such heavy topics, but compare that to a song like Disappear, which has simple, beautiful lyrics that also deal with loss and the difference in quality is immense. I hate to be down on MP's lyrics for that song, but I think he could've done better. Also, the song is too fucking long. I could easily lose a few minutes of it.
-Tuscany. Worst concept and lyrics for an epic aside, the music is really cool. The ambient section doesn't really do much for me and could be shortened or made into something a bit more lively, but nothing really feels wasted on this one. I think there's a unnecessary 0:45 silent outro on this one which bugs me because it only serves to make the song longer for absolutely no reason.
In short, this album is probably their worst alongside Octavarium. WDADU and FII always seem to rank lower than this one, but they're light-years ahead in every single aspect (except maybe production in WDADU's case).