I don't know if this would be any help, but I have found that I don't like Adobe Media Encoder. I usually prefer to render out a DV AVI file and then transcode from that to an MPEG2 file via Sorenson Squeeze.
The DV AVI file would be fairly large, and larger of course if you went uncompressed AVI, but maybe the two-step process could yield a better result. Do you have any other encoding software you could try instead of Adobe Media?
Two thoughts on the staircasing in the HD footage: have you tried deselecting "frame blend" or messing with any of the field options for the clips? I know that 1080i footage renders the upper field first whereas 720x480i footage does lower field first.