Better talent around him means he hasn't had to carry as large a load.
Duncan has also just been healthier. KG's knee injury in 2009 has contributed a lot to his decline. Maybe Duncan has taken better care of himself, but I doubt it -- KG seems pretty fanatical about keeping himself in shape.
To me, the biggest thing is Duncan's nickname: Mr. Fundamental.
Tim Duncan has always had better fundamentals. While both players were imbued with unreal physical gifts in their prime, Duncan has never had to rely as much on his athleticism in order to play his game.
KG also is much more reliant on his jumpshot in order to score, whereas Duncan has a much better inside game. So even when Duncan is tired and his legs aren't there for a jumpshot, he can get inside and get a shot or get fouled.