All things considered, I'd say Emerald wins it for me. I think Hoenn is the best region exploration wise, and the Emerald Battle Frontier was the best post-game content ever in my view.
Close runner-ups would be:
FR/LG: I love Kanto and I'm a huge fan of the Sevii Islands, which I think is also one of the best post-game contents, there was a chill atmosphere to it that I really enjoyed. FireRed was my first game (along with Sapphire) and I can replay it over and over again without getting bored. I guess the only flaw of these games (and the reason I've restarted FireRed probably more than any other game) is that there's not much else to do once you're done with the Sevii Islands quest. There was a sort of Battle Tower in one of the islands but it was pretty lame when compared to the Hoenn Battle Tower.
Platinum: this game is basically flawless in my view, and the Distortion World is probably one of the most original ideas in pokémon history. It's just that I prefer Hoenn over Sinnoh and the Emerald Battle Frontier over the Platinum one.
HG/SS: as someone who likes to have an extensive post-game I could only love a game with two whole regions, and HeartGold is my favorite Johto game. With two regions + 1 Battle Frontier, these games could've been perfect but they have at least 2 major issues in my view: the TERRIBLE level curve, which is a flaw from the original Johto games that can make them somewhat tedious to play at times ; and the fact that there were very few new places in Johto and Kanto (FR/LG were better in this regard because they had the Sevii Islands), plus the Battle Frontier was a litteral copy of the Platinum one.
X/Y: I've only played X for the first time last year and it kinda brought me back as a pokémon fan, I loved the atmosphere of the Kalos region, the mega-evolutions, and some of the pokémon were really cool. But these games have at least 2 signficant flaws imo: first, they're way too easy and there's too much hand-holding ; second, there's virtually no post-game. These games deserved a Z version, which could've fixed these flaws. Pretty sad that it never came out.
OR/AS: loved Alpha Sapphire because, of course, Hoenn is awesome and a modernized version of it was pretty thrilling to see. I loved to fly in the Hoenn sky, and the Delta Episode, oh my god... I would classify it as the most epic moment in pokémon history. Because as a kid I thought you could go to space in the original Hoenn games, through the space center, and catch Deoxys. Unfortunately you couldn't, but OR/AS made it happen! However, these games also have a few pretty signficant flaws: like X/Y, they're way too easy (I mean, they literally hand you a Latias/Latios for free, that's outrageous!
); and the post-game content is interesting in a sense because you could catch so many legendaries, but it was way too repetitive, you catched them all in the exact same boring way: go through a warmhole, that's it. And, of course, the most disappointing part of these games was the absence of a modernized version of the Emerald Battle Frontier.