Kudos, Nicky, for your extensive and informative listening profile! 
And interesting Dream Theater discussion earlier on in this thread (page 1). I love DT! I’m not sure a big change occurred between Scenes and Six Degrees, I think the change between Infinity and Scenes is much bigger. DT did a “Marillion” there (releasing an ambitious, complex, epic concept masterpiece after releasing their most poppy, record company influenced album), Infinity can be viewed as their Holidays In Eden and Scenes as their Brave (and to draw the analogy further, Six Degrees as their Marbles).
Very interesting comparison. I must confess that I prefer
HiE to
Brave and
FII to
SFAM but, as you can see with my avatar, I don't have problems with albums with a more poppy/commercial approach
The difference between the two bands is that Marillion still uses and outside producer when Portnoy and Petrucci handle the production duties since
SFAM.
It's also amazing to see that, despite playing totally different kinds of music, Marillion and DT share a lot of fans.
By the way, am I the only one to thing that Petrucci's solo on
Take away my Pain is pure Rothery
My thoughts on their albums (from I&W onwards, don’t have their debut):
Images And Words: Great songs, but I don’t like the polished production, least of all the horrible thin ‘80s plastic sound of the drums (ABWH comes to mind with Bruford on the electronic drum kit). But not to be dismissed as it is one of the foundations of progressive metal.
Awake: The first DT album I got, blew me away and still my third favourite DT album. A lot more heavy and aggressive than I&W and a much better production, a more organic and less polished sound. Maybe because I started with this one and got to know I&W later on the latter was a bit of a disappointment. And to all the critics who say DT’s music is void of emotion: just listen to Space-Dye Vest!
A Change Of Seasons: The title track is a great epic! I don’t listen to the live songs often.
Falling Into Infinity: Their most "commercial" one, but still good. Love Trial Of Tears and Peruvian Skies.
Scenes From A Memory: They wanted to do a classic concept album DT-style and succeeded marvellously! My favourite DT album.
Six Degrees Of Inner Turbulence: Stunning album, although I prefer and mostly just listen to disc 1. My fourth favourite DT-album.
Train Of Thought: They wanted to do a classic metal album DT-style and succeeded marvellously! My second favourite DT-album.
Octavarium: I’m divided on this one. It’s a good album but it doesn’t really capture me somehow, don’t know why as it does have all the ingredients and great songs.
Systematic Chaos: On my shopping list, the snippets I’ve heard and the reviews made me drool. 
If I had to make a ranking of DT albums, it would be :
1. I&W : Wonderful from beginning to end (agree with you on the drums sound, though). Definitively a classic of prog-metal
2. SDOIT : their proggiest and most versatile album. A double CD with zero defect (well, OK,
Misunderstood could have been two minutes shorter) !
3. FII : it has its ups and downs but the ups (especially
Lines in the Sand and
Trial of Tears) are very, very up ...
4. ACOS : great epic and very emotive Elton John's covers. The other covers are good too.
5. Awake : a dark gem but I must admit that I don't play it so often because the most metallish (?) songs don't fit my taste (
Lie,
The Mirror,
Scarred)
6. Octavarium : very eclectic. Honestly, there is not one song on it that I don't like but so far, I don't see the masterpiece that others see in the title track
7. Systematic Chaos : it lacks a bit of eccentricity but all songs vary from good to excellent. I think an outisde producer would have helped, though
8. ToT : I'm not a metal fan so it's not easy for me to swallow this one in one piece but I also lack the great melodies that fulfil their other albums. But every DT fan has to have it, at least for
SoC 9. WDADU : good debut album with lot of promises but, all in all, it's just an average heavy metal album IMHO
