The bike is definitely set up too soft for rider's of our manliness, especially the rear.
There is no doubt you would improve the capability of the bike by matching the springs & hydraulics to you weight & riding. The question becomes do you need it to be more capable? For me riding in AZ, there will always be surprises in the trail. Having some "reserve" in the suspension has saved my bacon when I had more momentum than talent more than once.
Racetech's suggested spring rates are here:
http://racetech.com/ProductSearch/1/Yamaha/WR250R/2011