The three game have same plot line, but time and darkness were released first, then Sky was released later. Sky is better than those two. Time and Darkness have their exclusive items and Pokemon.
Exclusive Items :
Time - Vile Seed, Foe-Hold Orb, Sun Ribbon
Darkness - Violent Seed, Foe-Seal Orb, Lunar Ribbon
Exclusive Pokemon :
Time - Riolu, Lucario, Pacirisu, Combee, Butterfree and Mythical Pokemon Celebi
Darkness - Buneary, Lopunny, Rotom, Burmy, Beedrill and Legendary Pokemon Mewtwo
Time's exclusive Pokemon Riolu evolves with Sun Ribbon, while Darkness' exclusive Pokemon Buneary evolves with Lunar Ribbon. Sky has more content, new starter Riolu and Spinda Cafe. In Spinda Cafe, Spinda makes juices from Gummis, Seeds, etc. And Gummi juices raise IQ and sometimes Stats. Wynaut on the right side recycles any items for things. It has Wonder Mail renamed as Wonder Mail-S. Bottles containing Wonder Mail-S are sometimes found in the beach. It also has Special Episodes that are unlocked as you progress in the story.