Okay, let's see...
1. Black 2/White 2 - You guys know me. Lots of Pokémon to use, cool new areas in the Unova region, Ghetsis trying to physically harm you, Iris having a sick battle background and theme, and the post-game. I could go on and on about how I love this game.
2. X/Y - Yes, even today I still love this one. Customization, lots of Pokémon, opponents that I tend to get tripped by.
3. Omega Ruby/Alpha Sapphire - Has quite a bit to do, and they improved some of the weaker things about RS (better characters, Pokémon are more fun to use, and 3D makes it even cooler).
4. Black/White - Plot, only new Pokémon, some difficult battles, this one really does it for me. If it weren't for its fandom that sometimes makes very jarring claims about B2W2 being the same, this would probably be #3, but it's still very good.
5. Platinum - Epic story, cool Pokémon to use, this one really does it in a lot of ways.
6. Heart Gold/Soul Silver - Great features and post-game, walking Pokémon, has some tough fights, there's a lot to do here. But not as good Pokémon to use makes it a bit worse than Platinum for me.
7. Fire Red/Leaf Green - I do enjoy these, and not just for nostalgic purposes - they do have quite a bit of areas to explore and I do find the Pokémon more fun to use.
8. Red/Blue/Yellow - Juggled between DP and this, decided this because I do still like various things about the original. Had to give it some credit.
9. Diamond/Pearl - This one did bring Pokémon into the next generation with 3D and things like the physical/special split, so I want to give this credit also, but Platinum outdoes it in basically every way.
10. Emerald - A little better than RS on their own, but I don't really care for the Battle Frontier nowadays.
11. Ruby/Sapphire - Don't really care about the mechanics now, Pokémon are not very fun to use since there's so few good moves, characters suck, etcetera.
12. Gold/Silver/Crystal - Not a lot to say about this one - not much development, battles are much too easy, training sucks. And they have full-fledged remakes too.