That's Quite Hard To Answer,Because The Story Of The Games Are Always The same.I'll Have To Say,Platinum Or Crystal.
Nothing beats Silver/Gold. I'm hoping HeartGold/SoulSilver can go one better though. Silver/Gold had so many features, and also introduced so much more new ones that we still see today. Including, Day/Night, Berries, Breeding etc...... All I can say is Gold/Silver has it all. If it wasn't for it's dying internal battery, Gold/Silver is still very playable today.
i would say everything past the first 3 are all the same. ok so theres a few more regions to go to and about a few more pokemon to catch. about 300+ or so to be exact. the point is all the same. not counting a few places to explore and a whole 5 year olds christmas list length (its quite long. probably longer than a college level essay lol) of pokemon to catch to get. get badges: check beat bad guys: check get through elite people: check congrats! now wait for another game to be released to do the exact same all over again. hmm, this reminds me of school. once you graduate, you go back to being a low rank in another school lol