I have the EII and the PE, and I agree that the main difference is the PE has better flare resistance. They are both multi-coated, so the difference will usually not be noticeable. They do not have an identical optical formula.
They are both the same size, and the EII seems to be a little heavier. The EII has a nifty-lookin' green stripe around it while the PE looks boring by comparison.
The stop down lever on the PE is chunkier and a little more annoying when turning the aperture ring, though the ring is wider and a little easier to grip than the EII's.
I've read that the EII was supposedly a noticeable improvement optically over the MC, but I have no direct knowledge of that.