Jones, ranked No. 1 among North American skaters by NHL Central Scouting, has ties to Colorado. He took up hockey as a kid there while his father, Popeye Jones, was playing for the NBA's Denver Nuggets.
Colorado said it liked Jones, but wanted to draft a forward.
The six-foot, 182-pound MacKinnon, who does not turn 18 until Sept. 1, led the Mooseheads to the Memorial Cup.
He topped the tournament in scoring with 13 points (seven goals and six assists), including a hat trick in the championship game, and was chosen tournament MVP.
The native of Coal Harbour, N.S., scored 32 goals and added 43 assists in 44 regular season games.
"What makes Nathan stand out is that he has a real quickness with his read and react: his hockey sense, how he sees the ice and his vision," said Dan Marr, director of NHL Central Scouting. "That is something special in a player. He is continuing to physically mature, but already he’s got a lot of grit in his game and he is a competitive player."