As a child I never got to play any other game than Pokémon Diamond, because I didn't have any excess money to purchase it. So I played that a lot and the nostalgia gives me so many good memories that I'd like to think it was my personal favourite.
But actually, since I've played each generation, I think the following:
Generation 4, the HG/SS games, were by far the best games in terms of gameplay. Even though it was a remake, the addition of always sprinting when the Running Shoes were on and the possibility of registering two key items were so simple yet so revolutionary, made my experience a whole lot better. It also had the most to offer: 16 Pokémon Gyms, an Elite 4 and Champion Lance and not to forget Red. There were so many legendaries to catch that you could be entertained for days. Lest not forget your Pokémon running behind you.
However, in terms of ambiance, no game other than the Black and White series are la crème de la crème. The OST is just the absolute best, epic music to accompany epic fights and the whole story of N is absolutely breathtaking. I loved to play these games.