Just got back from a long Baja trip, me on my WR250R, son on a lightly used but mostly stock DR650. Both bikes did the job, but my son will be looking for a WR250R the next time
Lower seat height, and 650 cc's are the DR's strong points--no replacement for displacement. That said, the WR's motor and 6 speed transmission didn't slow us down a bit. However, the DR bottomed out a few times on big rocks that the extra height on the WR allowed me to roll over. (We both were carrying roughly the same load.) The WR's stock suspension is much, much better than the DR. The fuel injection worked flawlessly while we had some carb issues with the DR. We both fell numerous times, and the DR was much harder to pick up. The DR's tail light rattled itself to death, the right side body panel melted and somewhere along the line the horn died as well. Worst of all, the clutch disintegrated in the middle of a wet dry lake...
The only issue I had with the WR was that the chain wore out and wore through the chain guard and slightly into the swingarm, but that was user error--I got complacent after the first 4000 miles and stopped checking the chain slack.
There's a lot of good things about the DR650--it's definitely fun to ride, but you'd have to spend a good chunk of money and time to get it in the same offroad touring trim as the WR, and it's still going to be heavy and low. I'd pick the WR 10 times out of 10.