I've never ridden a CR500 or a YZ426, although, given the opportunity I'd love to, so I can't give any comparisons.
I did have the opportunity to ride with a friend that had one of the first YZ400s', and his 400 and my 360 were very close acceleration wise. He's way out of my league in ability however, as he used to run the So. Cal. circuit as a 250 pro MXer.
I believe, from what I've heard, that the CR500 should have a much more violent hit than the KTM, and there-in lies the KTMs' advantage-a more usable power-band, just like the 4-strokes. This is not to bash CR500s'-that was actually my first choice when I picked up my KTM. It's strictly a matter of rider preference. That's why I made the statement, "ride the KTM380, then decide."