is that the only one? because layers have been around since long before Ravnica. was it the other way around before then?
No, copy effects have had first shot since the creation of the layer system.
I don't have any actual knowledge of what went through R&D's heads at the time, but if I had to guess, I'd say that even if the specific interaction wasn't possible yet when the layer system was created (I'm not sure whether or not it was), R&D would have been faced with a choice. By its very nature, the layer system's existence makes it impossible for R&D to reasonably print certain kinds of cards--how it's set up defines what kind of cards they can make. Color after type? Then they can't print "Green creatures are Elves." Power and toughness last? Then they can't print "Creatures with power 1 or less have flying". And so on.
If R&D set up the layer system to allow Volrath's Shapeshifter to work as expected, they either wouldn't be able to print any card that allowed players to copy anything with a
Control Magic-type effect, or they'd have to get rid of
Control Magic-type effects entirely. But if they set it up in a way that threw Shapeshifter under the bus, they would only be unable to create cards that could change what they were a copy of based on control of objects, which is of course a much smaller area of design space. So Shapeshifter got bussed.