Had to go with CK here. He's taller, smarter (37 vs. 28 on the wonderlic). Both are fast, both have great arms. RW has a better touch on his passes IMO. One thing I noticed with CK (and RW, for that matter) right off the bat is, unlike Alex Smith, he can throw his receivers open.
I suspect CK's 'fumbling the snap' problem was more due to weather in NE and was corrected in the second half, so I'd be skeptical of statistical analysis that points to the number of fumbles.
Right now RW runs the offense better than CK does, and that could make all the difference in the upcoming game.
CK has a slight edge in quality of receiving targets, both teams have decent WR's, but the 49ers have Vernon Davis (see how I didn't go with initials there?).
Hopefully this argument will go back and forth for years to come.