1. Autotune is easier to use. Melodyne interface is a bit arcane at 1st, certain amount of learning involved.
2. Autotune is faster to use, Melodyne needs a 1st round of prepatory work of "melody detection" before the editing can start safely.
3. Autotune is less hard to screw up in terms of sound. Melodyne adds a strange out-of-phase cancellation type of sound to my ears at least (I have used version 1 to now 2.6 it has improved slightly) but can mostly be noticed only when material is heard in isolation.
4. Autotune can only correct pitch. Melodyne can correct pitch, timing, volume, volume transitions, vibrato strength and more for each note and the adjacent ones. And it claims to be able to transpose 1 octave without much artifacts. My experiments tells me it is very much "material dependent".
5. Autotune is more convenient to use. Melodyne (even with the Melodyne bridge thingy) is still a step away from total integration with the host DAW.
That aside, I use Melodyne.
