The MC lenses aren't the latest Zeiss, but they don't suck. Some of the PE lenses, like the 150mm, are the MC lens with newer coatings. I think the 200 is the same. My 250 sure seems to be the same. Others were redone, like the 40mm, and might be better, though I don't know.
The 180 PE is a newer design and might be superior to the 200 optically. It definitely focuses closer.
I have heard that the 75mm MC was nothing special, that the E-II and PE (which supposedly are the same design) are superior optically.