See the funny thing about this topic is that it is VERY hard for anyone to narrow down such a question into one game, so I'll have to go with 3 of them (that's the most I could narrow it.)
1. Pokemon Y. When this game came out, I expected nothing too out of the ordinary. A 3D world wasn't too much to gawk at (for reasons I will explain later) and I felt like the soundtrack would be nothing extraordinary (I hold music very high in importance. :P). Boy, I was wrong. I LOVED the game. The plot, although short in feeling (probably just because I played through so fast) amazed me, the music was astounding, and the graphics were all around great, nothing really stopped me from liking this game and it hence became my favorite.
2. Pokemon Colosseum. Before Y came out, this game was the best thing I could play. I loved the darker plot in a sense and how there were no wild Pokemon and many other changes in game mechanics. It was also the first main series-esque game in 3D, which blew my mind with battle animations and all that. I loved the music, the design and pretty much everything.
3. Pokemon Emerald. This game was so great... All the improvements it brought from Sapphire and Ruby, battle entrances, Battle Frontier, PokeNav improvements and just... Everything! It always has been a great game and one of my favorites.