My first thought it that speed is pointless. HR is worth 7 points, while a stolen base is only worth 2 (-1 if caught).
[edit: did the math on Jose Reyes and Jim Thome. Last year Reyes would have gotten 567 under this scoring while Thome would have gotten 578]
I haven't done the math, but just looking at pitching is would still seem (even with 3 for inning) that a good closer would top a good starter. Have to do the math to figure it out for sure though.
[edit: did this math too. Based on last year's stats Johan Santana would get about 310 points and Todd Jones would get about 460]