And this is why I always say that fantasy football is creating an entire generation of idiot football fans. W's are all that matters.
This has been going on long before Fantasy Football became as popular as it is today, though I do agree with what you're saying. Fantasy has skewed many people's viewpoints in what makes a player good.
But no matter what, yards and flash will always edge out boring stats (boring to the common average joe anyway) like completion percentage, yards per attempt and QB rating. And really this sort of thing isn't exclusive to just football. Look at MLB this year.. the raw stats of HR's, RBI and batting average (Cabrera) beat out the underlying sabermetrics stat goodness of another (Trout)
Does Wilson deserve to be in the conversation for ROY? Absolutely he does! But he's very unlikely to do so unless Andrew Luck and RG3 get hit by a bus or punch a baby or something drastic happens.