Add some track based filter automation to the three sequencer tracks (open and close the cutoff and alter resonance on one of the patterns). I'm not sure I like it specifically, but it does prove that I can introduce longer-than-a-pattern automation to pattern based stuff.
The problem is it has to be done after the fact, so the automation can't be added early in the process - only after the tracks are recorded out to linear tracks.
I think Ableton's arrangement view allows more flexibility (but I don't really have any significant experience with it). Live seems more tuned for this sort of "scene" based composition – Logic's Live Loops are good, but not good enough… I'll probably end up using live loops as a way to doodle, but once I have enough of a germ of an idea, will probably be working in the track view and manually dragging new patterns into the tracks as needed.