I'll second the opinion on tires. The shorter harder tires make the ride really uncomfortable (to me). I run the factory 22" tires. They play a pretty big role in softening up the ride quite a bit. I think if you get a lighter and possibly a little bigger tire on there, you'll notice improvement.
Keep in mind though that the 250R does have the more advanced suspension setup (progressive linkage) between the two machines, so it isn't surprising that the ride is nicer.
- Frank
1984 200ES Big Red
1985 350X (x2)
1986 350X
1986 250SX
1984 Auto-X
1984 ATC70
1985 ATC70