You make some good points about why they are heavier now. The "numbers" are a bit misleading too, between years and/or brands. I look at the 06' CRF250X listed at 225 (dry) vs the 2012 at 253 (wet) and figure 20 lbs of that is the "wet" stuff.
Also, "where" that weight is on the bike affects the handling in a huge way, the lower it's placed the better. That was a big reason I sold my DRZ400S was because it was so "top heavy" and I always felf like it was trying to "pull me down" when things got tricky.
I think Dual sports are designed too tall also. The clearance & suspension is important for racing, but a lower saddle height makes a bike so much easier to handle and enables folks with shorter legs to ride them too.