Its like he's ONLY showing you technique, not actual music. If always preffered teaching (and learning by) taking an existing song, isolating a specific technique (say I'm teaching sweep picking), and explaining it in the context of the song.
Like when I start to get people into 'shred' techniques, a song I always point them to is Tony Macalpine's "Wheel Of Fortune". Its got alternate picking, its got sweep picking, its got arpeggios, its got the whole works... but its also a really good song (just to listen to if you will), so it gives people ideas right away.
Maybe I'm just not smart enough (or musically inclined enough) to follow Petrucci,