I just got a '06 WR450 and I have an '02 KTM 400EXC. The basic differences that I can see are that the KTM carries it's weight a bit lower, so it is easier to ride in the really tight stuff. Components are much better on the KTM, handlebars, controls, etc. KTM has better ground clearance.
The WR has a plusher ride, at least for me. Getting the KTM suspension to work right is a bitch. I had to go stiffer springs on both ends. I also had a bunch of blown fork seals on the KTM. That cleared up after I added seal savers.
The WR seat is worlds better than the three seats I tried on the KTM. The KTM totally screwed up my tail bone.
I had to add the optional fan to the KTM to keep it from boiling over. Unfortunately the thermostat for it is at the bottom of the left radiator right where it can get hit. I have had the electrical connectors break several times and I got a boil over every time due to the restriction that the fan adds to the right radiator. The last time this happened it developed a leak at the water pump which I have yet to fix. $35 in parts for that one.
One thing I didn't realize until the last couple of days is how much better the quality of the hardware is on the KTM. Allen bolts (KTM) vs. Phillips heads (WR). I've already stripped the head on one of the screws for the float bowl on the WR and I've only had it off twice. The hardware is also more consistent on the KTM size wise.
Oil changes are a snap on tke KTM and so is setting the valves. It took me nearly 2 hours to change the oil and filter on the WR yesterday. 15 minute job on the KTM. I don't know who came up with the oil circuit design for the WR, but I think they are on drugs.
I'm still dialing in the WR. The only thing I really hate so far is the front tire. A Dunlop
739 doesn't cut it in Ohio in the fall. I'm putting the Dunlop 773 from the KTM on tomorrow.