I don't know if this suggestion is rendered impossible by technical limitations, but I wish for two additional input options:
1) the option to send the signal from the stereo return inputs through the entire rig, and to retain the stereo signal throughout as well
2) the option to use the S/PDIF input as a stereo "front" input similar to my first suggestion, and send it through the entire rig. in stereo preferably, but even if it were summed to mono before going into the stomps that would still be a good option.
I've already stumbled across a suggestion for an S/PDIF FX loop but I am not sure if this has been requested or even denied.