Duncan leads in career points per game (and per minute), rebounds per game (and per minute), FG%, and blocks. KG leads in assists and steals. The same holds true for the playoffs.
Duncan has the better stats, and has won more. From my perspective, Duncan wins by a comfortable margin.
TP for posting the reasons for my gut opinion that it's clearly Duncan.
Having the better team doesn't have much to do with it. KG, throughout his career in Minny, and with us too, is not a go-to scorer. He is really better as a 2nd (or 3rd) option on offense. Old Pal Kevin McHale remarked once that the C's got it right by playing KG that way, and when Minny had success, they had Cassell and Spreewell to be the clutch scorers. I know KG's scored a lot of points, but he's not a #1 option, and never truly was comfortable in that role. (I might go so far as to call him a superstar-role player). One other factor on offense: Even in the post, KG just doesn't draw fouls. If the other team is going to get in foul trouble, it won't be because KG was aggressive and drew fouls. Jumpers and fadeaways score points, but draw no fouls. I'm not sure a team built around KG would have it on the offensive end to win a title...ever.
Duncan has shown to be a different, but still good big-man defender, and a better primary option on offense. His team was better, but he was still the #1 guy on both sides of the ball all the way to 4 titles.
I go with Duncan, easily.