Super.
Best gameplay by a mile, actually feels like playing a roguelike.
Best music, and while comparing compositions may be subjective there's no denying the fantastic sound quality compared to the DS tin can.
And finally it's packed with content. Five different towns while the others only had one, a thousand quests while the others only had like twelve and the rest were randomly generated and close to twice the amount of Pokémon.
Also, as someone who loves Sky I thought the story in Super was the best in the series, because it intentionally plays on your expectations. I get a little confused when people complain about Super having an unexpected twist and then praise shit like Sky's ending when it was just copy+pasted from the last game.