I learned images and words, and awake beginning to end. After those albums I learned probably an average of 2-3 songs off each album, except scenes, again whole album. For me personally the hardest part to play cleanly is the glass prison arpeggios. It's actually easier for me to use a mixture of the alternate picking, and sweep methods to play that section. I really expected that section to come easier to me, as I already knew how to play the entire Jason Becker perpetual burn album. Pretty much one huge arpeggio étude.
It's like anything else, some things that are harder for some, are easier for others, and vice versa.
The best advice I've heard on developing a unique style forcuses on that fact. Steve via said that as you are developing your technique, some things will come to you easily, and some will be difficult. He said to of course try to work on the difficulties, but more than that take the things that come natural to you, and accentuate them in your playing.