I'd have to say that on a practical level my favorite Pok?mon game would currently be Omega Ruby/Alpha Sapphire, specifically Alpha Sapphire since I prefer Archie over Maxie. Reason being that it was a near perfect example of the sort of games I want Game Freak to release. The major reason is the presence of Super Training, because I find Super Training to be extremely useful, time saving, and enjoyable enough on its own when compared to having to EV train the old fashioned way. There was a decent enough challenge provided and Elite Four scaling, both things which X & Y unfortunately lacked. It also had move tutors available, gave us more Mega Evolutions, let us fly around on Latias/Latios, and gave easier access to certain Hidden Abilities thanks to the Pok?Nav Plus. Heck, the Pok?Nav Plus allowed you to challenge leveled up versions of trainers you defeated in your journey as well, so that was great for grinding and earning money.
The only real negatives for me are the lack of trainer customization, since it was just introduced in the previous games and I wanted more, and the lazy reuse of the Battle Maison instead of bringing back the Battle Frontier, or at least the hinted Battle Tower.
Second place probably has to go to Pok?mon HeartGold since Pok?mon Crystal was my favorite Pok?mon game for years, and my affection for it is what brought me back to the series after I quit it due to peer pressure from Gen III until a friend told me about HeartGold and SoulSilver.
The whole game is enjoyable and is just full of content:
- Two whole regions to play through with 16 badges to earn.
- The Pok?athlon Dome minigames to enjoy and earn ribbons in.
- Getting to battle Red in the postgame.
- The ability to have one of your Pok?mon used Headbutt on a tree to try to reveal hidden Pok?mon.
- Learning more about Silver's backstory with Giovanni if you acquired the event Celebi back in the day.
Why HeartGold over SoulSilver? Because I prefer Ho-Oh's design over Lugia's
because of Lugia's gross looking hand wings and because I encountered my first non-Lake of Rage Gyarados shiny in this game, a shiny Gligar that I caught and have since evolved into Gliscor and sent up through the generations. That Gliscor sparked a love for shiny Pok?mon within me and I've amassed a collection of them over the years thanks to the Masuda Method making it simpler to acquire them. The only reason this is second is because it's older and lacks the convenience of Super Training.
Third place would have to be Black/White/Black 2/White 2 with no real decisive winner among them, though I lean more toward Black 2/White 2. Unova's a great region with a ton of great new Pok?mon and an enjoyable soundtrack. Heck, I'm one of the weirdos who actually likes the Vanilluxe and Garbodor evolutionary lines. These games were the first Pok?mon games which gave me the opportunity to trade and battle with other players from around the world, so the fifth generation holds a special place in my heart. I prefer the designs given to Hilbert and Hilda (the player characters) over Nate and Rosa from Black 2 and White 2. I also prefer the story in Black and White, and I prefer Alder as a Champion. However, I lean more toward Black 2 and White 2 because of the presence of the Pok?mon World Tournament, the presence of move tutors (and how affordable the moves were compared to later ones since you paid with shards), and because it's kind of neat to see Cheren become a gym leader, Iris become the Champion, and to travel around Unova a different way than you did in the originals with a few new places. They're overall strong games and, like HeartGold above, they're not higher because they lack Super Training as well. I really can't stress enough how much I like that feature.