Ages had a better storyline. Comparing the stories; a sorceress who goes from possessing the controller of time to travel to the past, to possessing the Queen of the land so she can order the civillians of the land to build a tower that reaches the heavens, so she can receive the power of the gods. Compare this to some big guy who kidnaps the controller of seasons, and then the seasons in the land get stuffed up. OoA definitely has a better story.
But I like OoS for it's gameplay. The bosses were better, the puzzles were trickier, and the game was just somehow cooler. Plus, Seasons was the first Zelda game I ever bought.