Well since I own one of each,

I can tell you what I See, with regard to stock "87" YZ490 and stock "01" KX500. In all fairness to the YZ490 it is an awesome monster for its time. If Yamaha had continued to improve the 490 it would be indeed a different story.
There is no question about the handling the KX is much more forgiving. The KX also puts the power to the ground much better.

I also agree with the comment about the YZ490's power band being similar to a 125, although I think I would compare it more to a strong 250!
The real challenge owning both, is to see how close I can get my YZ to performing like the KX!
The obvious place to start is with the power band, there is some pretty radical carb tuning that has been perfected, which I am about to make on my YZ, which is reported by people in the know to make a similar difference to the reed spacer in the KX.
My KX is no longer stock since I added a reed spacer and an FMF pipe. I also have a FMF pipe on my YZ so they are equal there. I am going to machine a reed spacer for the YZ in the next couple of weeks and see if it has similar results.

My buddies in the YZ club think I am on drugs, they just can't imagine how moving the reeds out 3/8" can do anything! Well will see about that!

No one makes them, so I may have something to sell my Bud's.
The YZ is much lighter in the front end and when you hit the power band and you have traction you might find yourself sitting on the ground in behind the bike.

The 490 has always had a problem with detonation, which I think has a lot to do with being air cooled, not to much can be done there.
Bottom line, what a fun project,

I wouldn't give either one of them up!

I love to ride them both!

The explosive power of the YZ490 is a blast to ride!
One more thing, The YZ490 starts ever time 1st or second Kick! Hot or cold 1 week six weeks!

I can't say the same for my KX, although it is a lot better with the reed spacer!

Alan
PS -
"Don't Make POO POO on the YZ490!"
--------"Godzilla Still Lives" "If you don't believe it come on down and try it out"