Disclaimer: Systematic Chaos is my 2nd least favorite DT album, the first being BCSL.
On we go:
WORST
Repentance - one of my least favorite DT songs. Maybe even my least favourite song...no, wait, that's A Rite of Passage. Boring, annoying, insanely repetitive, has this narcissistic vibe about it that I cannot stand in its lyrics, mood, and the weird "let's bring a bunch of famous prog/metal artists to say a line or two for 4 minutes" idea. Ugh.
Constant Motion - I first realized I don't like this song when it invaded my otherwise ecstatic experience of my first Dream Theater concert in 2009. People around me were jumping and having a blast while I kind of snoozed around, during this song and during A Rite of Passage (did I mention I HATE that song?), while I just didn't feel anything, not even in a live setting. It's nice to listen to, rarely, but it feels so much like something that would come out from a different band. A band that is made out of a bunch of musicians that aren't half as talented as DT. I enjoy this song the same way I enjoy the occasional Guns n' Roses or Avenged Sevenfold song.
The Dark Eternal Night - I've had the opposite experience with this one compared to CM. I used to kinda dislike it and it bored me in the studio version, then I heard it in Chaos in Motion (and it was still bad mostly because of the quality of that DVD), then the band started playing it again during ADTOE's tour and it was much, much better. Then it clicked with me.
The Ministry of Lost Souls - I believe bosk1 said earlier something about this song being a DT song "by the book" or so (sorry if I'm misquoting here). I completely agree, and it clicked with me much more. I like the way the song is written and the lyrics are occasionally charming, otherwise awkward.
Prophets of War - One thing I hate about numerous songs from ToT through BCSL (although I still love 8VM and really like ToT), and the reason SC and BCSL are my least favourite albums, is that many songs don't sound at all like DT. It's like they tried to mimic another band and forgot to give it their own spin, especially in SC and BCSL, less so in the other two. This song in particular feels like an exception to me. Plus, I love the kind of band(s) they "borrowed" the style from.
Forsaken - One of DT's finest "single-ready" songs.
In the Presence of Enemies - Pt. I is brilliant in its energy and composition. Pt. II is very similar to Ministry, in that it feels like a playbook DT song in its structure, but it also has a very distinct sound and feel and I love how big and grandiose it sounds. Put them together and you get an amazing epic. It's a shame they didn't, but I'll forver listen to the CiM version, or to my edited complete studio version.
BEST