The Nuggets and the Suns split the season series 2-2. But the two games won by Denver were prior to the KD trade, while the Suns won the last two games which were somewhat meaningless to Denver since they were more or less assured of the top seed in the West at the time.
I think Denver has the edge because of their depth. They have the players (KCP, Bruce Brown, Gordon, MPJ) who can help contain Booker and KD, but the Suns don't seem to have the personnel to defend Murray and the Joker.