Yeah, I flirted with the Yamaha 250F, but in the end you go with what you know. In some ways the WR would be better, but not as a do it all bike that must be kept and maintained for a few years. The 250 2-stroke is still the standard woods bike and the EC250 is the best 250, IMO.
FYI, a fully loaded '03 EC250 weighs 2 lbs more than a totally stock '07 WR250F, 1/2 tank of fuel each, same scale/method. So, with all its protection, the Yamaha will weigh more. Its a very nice bike though, in a different league than previous years.