Gens 3 and 5. 3 because Ruby was the first Pokemon game I ever played and my favourite Pokemon was introduced in Hoenn (Treecko), and 5 because of the more convenient changes (Such as being able to use Repels without going to your bag if the last one runs out) and the Unova games honestly taught me an important lesson about seeing things not in black and white, but in grey areas too. Also banger soundtrack and art style!
Originally it was gen 2 ever since gen 2 but I came to appreciate the plot and completeness of the gen 5 games to consider that my favorite generation.
That being said, after my recent playthrough of Ultra Moon I think gen 7 could take it. It has some of my favorite new pokemon, the games make for the most heartpounding nuzlockes, it has the best soundtrack (maybe tied with gen 4), you still had the option to turn exp share off, and I just love the experimentation and cultural exploration.
Edit: now that I am thinking about it I think odd number generations have aged better than even numbered ones
While HeartGold has a special place in my heart- pun not intended- due to being my first Pokemon game, Gen V has my favorite story, the most Pokemon I love [literally there's only like. 1 or 2 gen 5 Pokemon I actively hate. Most I love, like, or at least can appreciate], N... ngl I was an N fanatic as a kid. Literally one of my favorite Pokemon cards is N's Zorua from Journey Together! Specifically, the one below.
It's so cute! While I adore Gen V, none of the Pokemon from that game make the top cut for me. My top 5- the most zoomed in I can get- are Chikorita, Meganium, Crobat, Shinx, and Luxray. But I love so many Pokemon that making a top 10 would be near impossible.
It's an unpopular opinion but I really like Gen 6... Legends Z-A finally gave us some clousure to the whole story! It's just such a beautiful region with beautiful pokemon. And it has Sylveon!
Gen 4 is my favourite. A main reason for that is definitely nostalgia... But I'd argue the secret hideouts from that gen are objectively great. I was so disappointed when they remade Pokemon Pearl and Diamond for the Switch and didn't do them justice imo.
Gen II. The launch of Silver and Gold was super exciting to be around for. Pokémon was booming in popularity and we learned that new Pokémon were being introduced beyond the original 150, the games looked so much better than Gen I due to being released on the Game Boy Colour, and we had the debut of the breeding mechanics and day/night cycle. But the most exciting part for me is that after completing the Johto gym challenge we then got to go and re-explore Kanto!
It's probably nostalgia talking, but it felt like a huge leap. But I enjoyed playing SoulSilver just as much as the original. I'm hoping for a revisit to Johto on the Switch at some point (and not a port like FR/LG!).
V is a longtime favorite of mine. I loved the games and I loved the way that they made only new Pokemon available before the post-game in B/W. It was so refreshing for me because up to that point in playthroughs I stuck with a lot of the same Pokemon if I could find them.
Also, I find Gen V to have a large amount of top favorite Pokemon for me like Deerling/Sawsbuck and Samurott.
Gen II was the best back in the day. I've never played a sequel to like anything that I loved as much as G/S/C back when they came out. But they're dated now, of course.
Gen VI is up there for me, too. I love a lot of the Pokemon, I love Kalos, I love its OST.
Gen VIII houses a lot of my top favorite Pokemon as well and I like Galar. But I understand that people found the games underwhelming. I've been no fan of having games that don't let us have every Pokemon and Gen VIII was where this sad trend started. So Gen VIII does not make it as my favorite even though it has strong points for me.