Alpha Sapphire is, by far, my favorite 3DS Pokémon game. Funny, even though I initially stopped playing the main series after Gold and Silver many years ago, I decided to return to the franchise in early 2015, by picking up a 2DS and a copy of Alpha Sapphire, and come to realize, I actually enjoyed the Hoenn region and the gameplay features of this remake (despite the many criticisms ORAS has received since its release.)
3DS? I honestly liked all of the games pretty equally, but I'm tempted to say Alpha Sapphire. I loved Y because it changed so much about the core games and added some of my favorite Pokémon of all time (Aegislash and Tyrantrum), but I honestly enjoyed Sapphire just a bit more. Ultra Sun is a lot of fun too, though!
All the 3DS titles are great but I had most fun with ORAS. I own both games and played through them at least 2 times each. They're my favorite remakes so far. I just love the changes they brought into those games without completely losing touch with the originals. Ultra Sun is a strong competitor though.
I really liked Moon... mostly because I have more good memories with it compared to the other titles. The online competitive play was lit, I got way too into breeding perfect mons, and the experience was something nice and fresh. I knew what to expect with ORAS and USUM, but Moon was different and was the most enjoyable of the bunch.
Ultra Sun, only issue is when you have to use Lunala to go into the ultra space, I find Solgaleo easier to maneuver. I like the Hoenn games and remakes though bc Archie and Maxie aren't really that bad? And they get good redemption in ORAS too, they're more lighthearted games.
USUM. Mainly because it improves the pacing of the early game and has more Pokémon variety. The major changes aren’t quite enough to call it a “new game,” but they do make it the definitive Alolan experience.
