Of the two games, I think Oracle of Ages is the better game. There were many similarities between the two games, like the graphics were exactly the same, and a lot of the music was reused between the two games.
Oracle of Seasons and Oracle of Ages focused on two separate aspects of Zelda. OoS mainly focused on tough enemies and bosses, while OoA focused on challenging puzzles. I personally like solving puzzles more than beating up hard enemies, so this counts a lot towards why I like the game more.
Fun items is another thing I like in Zelda games. Of the two, OoS probably had the better items. OoS also introduced one of my favorite items, Roc's Cape, which was not present in OoA (only Roc's Feather was present in that game).
The games also revolved around a central item. In OoS, it was the Rod of Seasons, which allowed you to change the seasons to gain access to other parts of the overworld. One of the main objectives of the game is to gain the power of all the seasons, so you can change the season to your will. OoA had a harp, which also serves as the main instrument of the game. The Harp of Ages allowed you to travel between the present and past to gain access to different parts of the overworld, or even change bad things that happened in the past so they are good in the present. Naturally, one of the main objectives of the game is to learn more songs for the harp which allows better transportation from the present to the past. The Harp concept in OoA appealed to me more, as time travelling is always an interesting concept. The time travel was improved from what we see in OoT, as we get to a point in the game when we can use this time travelling (almost) anywhere.
And probably what I look most forward to when playing a Zelda game, the dungeons. I would have to say that OoA had better dungeons. I felt that this game had better dungeon layout, and were more fun to play, and gave you a greater sense of accomplishment when completing the dungeon. OoA also had the infamous "Jabu-Jabu's Belly" dungeon, which is probably the hardest dungeon I have played in a Zelda game till today (no, I have not played AoL).
So most while there are some aspects of the games where OoS is better, I feel that OoA is the better game for the most part.