I am going to be annoying and choose several different games. I cannot pick just one!!! I've played almost all mainline pokemon games besides Ultrasun/Ultramoon. To this day, my fave's gotta be Emerald, Platinum, or Soulsilver. Those three stole 500+ hours each from me as a child. Recently replayed Emerald and it still was such a blast; I am sure extreme nostalgia bias also plays a role in this, but fuck man. I like that it is still a challenge, I love the story, I love the vibe, and the post game? Cmon.
Platinum still is so special to me because it really perfected what was child-me's favorite pokemon game (and the first game I ever pre-ordered), Pokemon Diamond. Platinum still has that special feeling that only Sinnoh has, without the struggles of the OG games. Plus, all the content and story added was delicious. The multiplayer, Wi-Fi plaza, etc. Man I just cannot get enough. And we are fortunate enough to live in a time where you can still access all it's special events!
Soulsilver is the only one I feel like I can confidently say "is the best" without the nostalgia being a factor. It is beyond a complete package. It really makes the last decade of releases feel sore for me, because in sheer terms of content, there just has not been anything close. It is INSANE that they packed all that in onto a DS cartridge, and then NEVER PORTED IT. CMON. I am so fortunate to still have my OG copy, because the price for this game now is just so stupid. I hope one day there is an easy way for everyone to play it (not including emulator of course), because I am sure there are a lot of new Pokemon fans that would really enjoy it. It really made the Pokemon world feel so big.
I also think that the Mystery Dungeon Explorers of Sky or Pokemon Ranger games should be considered, too. Those were incredibly enjoyable experiences in their own right. (Side note, isn't it crazy how premium the Nintendo DS's library is?)
And to even it out, if I am picking a modern Pokemon game, it's gotta be Pokemon Shield. Even though it really hammered in the trend of Pokemon's technical struggles, I genuinely enjoyed my time with it. I liked the wild area, the raids, Dynamaxxing was hype, the music was great, actually good character customization, and there are some seriously great looking locales. And I hate to say it, but the DLC is a must. It makes the game actually feel.. "full". The game is at its best when you are playing with your pals, doing raids. Some of the most fun I've had since Diamond/Pearl/Platinum's underground. The game is wayyy too easy though. I thought this was just a symptom of me having played the series for 20 years, but no man, when I played Emerald, that shit was still a challenge! The new games are way too easy!