There's a few, but first and foremost, for me, would definitely have to be Pokémon Emerald. Love all maps, music, and characters that they have--they're all unique and different in their own, respective way--and the plot this game carries is super-engaging. Plus, unlike Ruby and Sapphire, this game's also got access to a place known as Battle Frontier, which I remember having a ton of fun exploring.
Up next are X and Y. Although they do kind of lack in terms of storytelling, but what makes me like these two games is their features. One's got to be player customization, which is something I've always wanted to see in Pokémon games.