I've said alot on what makes a bad Pokemon game so lets see what makes a good Pokemon game.
Game Mechanics
Gen 7, the peak of good Pokemon mechanics, as it should be.
New Pokemon
Gen 3, all round they had it best.
Legendary Pokemon
Gen 3, They felt positively epic to watch.
Anime
Gen 4, Sinnoh was the anime at it's best.
Gym Leaders
Gen 1, The original 8 was just something special.
Elite Four
Gen 6 certainly gave them a unique personality.
Champion
Gen 4, not only best champion but best trainer in the franchise.
Rival
Gen 1, Gary Oak is just timeless.
Starters
Gen 3 is the only Generation where you can consistently build balanced teams across all starters.
Evil Team
Gen 9 had the most sympathetic evil team.
Evil Plot
Gen 6 wins it for sheer crazy.
World
Gen 8, Galar looks amazing but I am British.
Player Character
Gen 3, the only Generation where both are equally well designed.
Post Game
Gen 2, After the Elite Four, hey it's Kanto!
Navigation
Gen 4, Felt like a real journey with Mt Coronet.
Best Value
Gen 1, Pokemon Yellow as a companion to the 1st Gen.
Pokemon Professor
Gen 1, Professor Oak is timeless.
Best Plot Point
Gen 4, the Darkrai backstory.
Difficulty
Gen 2 has the most consistent difficulty curve.
Overall Best Game
Pokemon Gold and Silver
No contest, no other Generation has ever offered so much.