I know what you guys mean about the fender looking like its pointing at the sky. It took me a while (very short while) to get used to it. Then, after reading your guys' posts in this thread I started looking at some other bikes. It turns out that there is hardly any difference between the way the fender fits on a KX250, and on the KX500. I think that its just the difference between the looks of the stock 500 fender and the 250 fender. For example...
KX500 with a KX250 rear fender...
And a KX250...
Not much difference at all with the angle of the fender. I think maybe it could be the profile of the seat and tank too. If the big 5 had a flatter seat and low-profile tank it would probably flow better.