I probably wouldn't object to multi-wire branch circuits if it were common to keep them together, and label, but all too often I'm doing a service upgrade and there is a conduit with five circuits and only three or four neutrals. I can either put the circuits on the same leg they came from in the new panel, or burn a few hours tracing wires.
In other cases it is a three wire romex or BX and it's obvious. I twist the wires together right up to the breakers where a non-professional will probably notice something is meant to be that way.
Dave
