Fun list. Thanks for the work!
On the subject of Systematic Chaos: When it came out I absolutely loved everything about it. It was so refreshing after the disappointment I felt toward Octavarium. I rocked out to the entire album non-stop for months. Not long after their tour started DT cancelled a concert in my town and I started frequenting MP.com to commiserate and be around other fans.
Wow, was I surprised to find out that not only was I supposed to hate nearly everything about SC I was completely daft for having Ministry of Lost Souls as my favorite. If I found myself singing along with the fictional story based lyrics I should consider myself the meanest of rust plagued anchors dragging down the very notion of Dream Theater's nobility. The prevailing attitude from the majority of self-proclaimed 'DT's biggest fans' was shocking. Needless to say, I've had a hard time un-reading these opinions and they have forever tainted my enjoyment of the record. Slightly. I'm not proud of being influenced by others, so...
I applaud your list proudly placing music where you feel it should be. At the time of its release I would have placed SC in exactly the same place you have it now.