Yeah. Like you might have it operating as a +2 octave whammy using pitch glide on the first stomp, have it also controlling the cut-off frequency *and* Q of a filter on the second stomp, and finally controlling the feedback level and/or delay time and/or wet volume of a delay on the third one. Or other stuff like that. You can also use it as a two-state switch on some effects, like changing the pitch of a synth from one octave to another (I have one patch where I have a square wave bass synth on the heel position, then a square lead synth (+1 octave, open the synth patch's filter up a bit) on the toe), or having a different harmony note (or different key, or both) set on toe and heel positions on the smart harmony patch.
To me that's the best feature on the M9. Oh and you can plug in a second expression pedal if you want tell it which patches each pedal will be in charge of (you can set this per scene). Unfortunately I don't think there's any way to have each pedal control different params on the same effect, but maybe someone else who's actually got two expression pedals can correct me!