I have both, I use the Mission with a toe switch to do volume swells, switch to turn on a wah. I am really used to the old Vox/Crybaby style wah pedals, so I like the feel of it for that.
I use the Fractal one to do all other sweepable parameters, such as the speed of my univibe or rotary speaker, the amount of ring modulator, pitch shifts, anything like that. Some patches use that one to dial in distortion or delay depending on how wacky I might be feeling at any given moment. Wackiness aside, the feel of the Fractal one is like stepping in butter. Depending on your attitude toward butter, I suppose.