There are a lot of Pokémon games I like, so in an attempt to limiting myself, I've voted for only there.
First and foremost would be Emerald version. I'm a huge fan of Pokémon Ruby and Sapphire, and loved each and every minute of their play-through. This one, however, brings all of the best things from both those games into one, and top it all off, adds a few extra. Loved how they'd switched up May's and Brendan's outfits here, and introduction of Battle Frontier was very, very awesome. When I'd first visited this place, I've spent almost about an hour exploring, to see if I could find something interesting and whatnot. It was a very fun experience.
Up next, is HeartGold and SoulSilver. Similarly to above, I love Gold, Silver, and Crystal, and these two versions include all content that they contain, but in modern-day graphics and mechanics. They've also added a ton of new features here, with one of my most favorites being following Pokémon; adored seeing one of my team members walking alongside while travelling. I'm not sure if such a thing will ever return, but I hope it does at some point in future!
As for third, it's Pokémon X and Y. These two had given us ability to customize our players, which is something that I've been wanting to do for a long, long time. Only thing I dislike, however, is length of their story, which was sort of short. If it were longer, I probably would have liked it more.