1st Place: Pok?mon Omega Ruby & Alpha Sapphire come to mind immediately, so probably them. I had initially missed out on experiencing the original third generation games because I was in a phase where a combination of getting older and peer pressure had me stop getting new entries in the series from after Crystal up until that was remade with HeartGold and SoulSilver (though I did purchase Ruby, Sapphire, Emerald, Fire Red, Leaf Green, and Platinum and experienced them later). Omega Ruby and Alpha Sapphire were a great first impression of Hoenn for me, I'd say. It had a ton of modern conveniences like X & Y's Mega Evolution gimmick, Super Training, and easier and faster IV breeding thanks to the Destiny Knot. The Vs. Seeker allowing you to rebattle trainers was great and I got a lot of use out of that. I wouldn't say they're hard, no Pok?mon game is, but they felt more challenging or at least engaging than X & Y. It was especially nice that the Elite Four and Champion had their Pok?mon increase in level for rematches against them since X & Y totally ignored that aspect. The wormholes allowing for easier acquisition of legendary Pok?mon and the opportunity to encounter and hopefully capture shiny versions of previously shinylocked legendaries was fantastic, and flying around on Latias/Latios was a nice way to travel. Omega Ruby and Alpha Sapphire aren't perfect, the absence of the Battle Frontier with a cheeky sign advertising that it was coming soon and just copy and pasting the Battle Maison from Kalos even though that makes no sense was a real disappointment. But aside from that, they just have a ton to love about them.
Of the two, I favor Alpha Sapphire since I prefer Team Aqua.
2nd Place: Ultra Sun and Ultra Moon are strong contenders as well, I guess I'd put them in second place. Something about the original Sun & Moon left me feeling very underwhelmed and I almost didn't want to bother with Ultra Sun and Ultra Moon at first, but I'm glad I gave them a chance. First, they had the strengths of the original installments: Z-Moves, Island Trials shaking up the gym system, trainer customization returning and allowing you to finally take off your hat, not having to worry about losing moves because your Pok?mon no longer leveling up in the Day Care, how insanely fast it is to EV Train with a combination of Pok?rus, the Power Items, and SOS Battles, and being able to fight challengers as Champion of the Pok?mon League for the first time is really nice. As for new things, Mantine Surfing is a nice way to grind out Battle Points to use for the Move Tutors, Rainbow Rocket is more postgame content, Ultra Wormholes are neat and the addition of cool new Ultra Beasts like Blacephalon and Naganadel was appreciated. While the story isn't as good compared to Sun & Moon (though that's never been the series strongsuit anyway), I really came around on Generation 7 and appreciate them way more now.
Of the two, I tend more toward Ultra Moon because I prefer Lunala, though Blacephalon does make the choice hard.
Third Place: Black & White/Black 2 & White 2 would be in third place. They each have their own strengths. The story is way better in the original Black & White and I far prefer Hilda and Hubert's designs over Nate and Rosa's. That said, Black 2 & White 2 introduced new areas to Unova, gave us the Shiny Charm to strive toward, featured the Pok?mon World Tournament, and had the most convenient Move Tutors in the series. My general appreciation toward remakes and second installments is in full swing here. I enjoy Unova and they were the first games where I could access wi-fi and trade with people. I'm one of those people who was totally cool with their omission of the previous Pok?mon and giving us a region full of its own unique Pok?mon, and it's not that uncomfortable if you really want some of your old favorites since you can transfer the older ones up (granted, I do tend to get multiples of the games, so this would probably be a bigger issue for others). They were also the last games to feature the old sprites. They're ranked third because for all of their strengths, they lack the amazing features that Generation 6 brought. You can't really fault them for that, but it does diminish my enjoyment of them regardless.
Of these, I prefer Black/Black 2 because I prefer Reshiram over Zekrom.
Fourth Place: X & Y, for all their faults, were also enjoyable for what they were and I have to include them among my favorites, so they get fourth place. They laid the groundwork with the mechanics that I liked that I laid out in the paragraph about Omega Ruby and Alpha Sapphire and they introduced trainer customization, so that was awesome. I enjoyed exploring the region itself and I liked working at the hotel in Lumiose to earn money. Lysandre is among my favorite villains in the series, though Team Flare itself is really dumb. The postgame was lacking, but I did enjoy the Looker missions while they lasted. They were also, on a personal level, the first games in the series where I completed the Pok?dex and earned the Shiny Charm so there's that good memory associated with them too.
I don't think I lean toward one or the other this time, they're both good.
Fifth Place: Finishing up, I'll give HeartGold & SoulSilver fifth place. They're great but also flawed. Like Black & White, for as much as I love them, I can't love them as much as my absolute favorites now because of the advancements the series made after these games. The level grinding for Red is atrociously unbalanced and they replaced the awesome Kris with the terrible Lyra. Despite that, they're fantastic games otherwise. Crystal was my favorite game in the series for years and it tided me over in those years where I had stopped buying the games, so HeartGold and SoulSilver being better versions of Crystal in every way was and is beautiful and they're what got me back into the series. This post is long enough so I don't really want to list out all of the great stuff from Gold and Silver, but the Safari Zone addition was a nice touch and I got some enjoyment out of the Pok?athlon Dome. The extra content you see regarding Giovanni and Silver if you had acquired Celebi was also really fun.
Of the two, I prefer HeartGold, for a few reasons but strongest among them probably being that it was the first game where I found a (not Lake of Rage Gyarados) shiny Pok?mon, a shiny Gligar that I evolved into Gliscor at the soonest opportunity, and that sparked a love of shiny hunting for me for years to come.