My wife has a CRF250L (I have a WR250R). I'd say that the WR has a little higher build quality, but it's minor. The CRF has slightly better low-end torque, but doesn't rev as high as the WR. I've noticed that this has an effect when with knobbies (both bikes run D606 rear, MT-21 front) when at highway speeds (55 to 65 true mph). That said I also changed my sprockets on the WR, so that might have an effect, too.
The biggest knock on the CRF is the rear shock. It's not adjustable or rebuildable. Undersprung even for her and especially when carrying gear. She's about 60 lbs lighter than me. I'm not sure, but the new rally version may have a different rear shock. We ended up getting Racetech to redo the front suspension when a seal started leaking. I got her a very nice Racetech rear shock w/ external adjuster. Both tuned for her weight. Made a huge difference on handling and performance. Went from "I'm not liking this off-road" to "when are we doing another trip."
On the WR, I did get the rear shock rebuilt and had a new spring installed (see Go Race in Virginia - great company, full disclosure -went to high school with the owner). But the rear on the WR is adjustable and wasn't nearly the issue as with the CRF. I could have been fine with it in stock form, but did like the improvement.
Overall, the CRF is a fine 250 dual sport, but the suspension can be an issue depending on the Rider and intended use. Both our CRF and WR have had a lot of other farkles, but that's pretty normal. HDB handguards, risers and new handlebars and heated grips for comfort. 12V powerlet plugs. Plus pannier and tail racks for carrying gear and Rotopax spare tanks. We're keeping them for a while. Both are solid and have been very reliable.
Eville Rich