I've been using Photo Mixer for a while now (if infrequently). The new features on my wishlist would be:
o "Smart dot adding"
o A way to shift a photo as a whole so that it lines up with the other photo. (Failing that a good tutorial for how to "prep" photos in a standard photo-edit program before putting them into the photo mixer)
o A way to compensate for the two photos not having the same aspect ratios
o An easy way to adjust the Photo Mix amounts in units larger than 0.01%
o An "options" box (possibly tabbed) that puts the morph options, timeline options, edit prefrences etc. all on one place.
o An option to syncronize the zoom on the start & end photos.
o A way to easily tell which dots are faded - maybe a "select all dots faded to start/end/mixed"
o A "pick dot color" option for selected dots, rather than just "next/previous color"
o Allow user customization of the "default" layout. Maybe a "use this layout file when creating a new layout" option.