As of today I own both models. I am planning on doing a side-by-side evaluation of IQ of the two as soon as I can.
Technically they have the same optical design. There are some cosmetic differences in the exterior portions of the lens - beyond the red seal and other WR specific parts. Additionally, there is some information that the WR lens has slightly different coatings than the Ver. II model to enhance the front elements ability to shed water and not impact IQ. Both have quick shift, both come with hoods, both take 52mm filters, have metal mounts, etc. The WR version is 10g heavier than the Ver. II model and 30g heavier than the DA L model. Each of them has a minimum focusing distance of .25m, all have 11 elements in 8 groups, and are f/3.5 (5.6) ~ f/22 (38).
You can see from these pictures the cosmetic differences between the two lenses exteriors.