From what I've seen of them, DT always try to play a little bit of every "flavour" from their back-catalogue. With the exception of Portnoy's rotational-setlists - it looks like they're meticulous with their choice of songs and trying to play something for every individual fan (not to mention a large portion must be dedicated to promoting their newest album!)
I like the way you've read into it, and it does appear understandable.
I like your thoughts into the Black Clouds album cover especially - and I'll agree that DT themselves seemed strained in the making of and touring for that album. You might be on to something at least. :)
The first Dream Theater song I'd ever heard was In The Name Of God at a party a few years ago. I bought Train Of Thought and have since collected all of their other works. It's all fantastic!