It does reward tournament winners, but it is highly dependent on region/country. I think Daigo's 2nd place and 3rd place finishes in Japan were more impressive than his Australian and Portugal wins, yet he has way less points for the 2 Japanese events combined against just one of those wins.
Beating Nemo (2x), GO1 (2x), MOV, Haitani, Kazunoko, and John Takeuchi gave Daigo 96 points. Beating Ryan Hart, CCL, and Digos gave Daigo 128 points. How do you know which events should give out more points for a certain region/country? Well, which tournament would you assume would be harder before the tournament season was announced? Japan or Portugal? Everyone would say Japan.
Either Capcom need to change the way points are in certain countries or regions, or they need to give some countries more events. You may say everything is fair due to the equal amount of events, but some tournaments are flat out much harder to win.