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It's three years between the story of R/B/Y and G/S/C. You can guess at what happened in these three years if you look at the changes that happened in G/S/C's Kanto compared to R/B/Y's Kanto. Things like Koga becoming an Elite Four member and giving the Gym to his daughter, or other examples like that.
It's 3 years, funny thing is is that the story of Ruby/Sapphire/Emerald happens at the same time as Red/Blue/Yellow. So Silver/Gold/Crystal actually happens after Gen 3.
Yes, because at the start of Diamond/Pearl/Platinum, you hear about a raging Gyarados at the lake of rage. So R/B/Y and R/S/E happen at the same time, then three years later, G/S/C and D/P/P happen at the same time (: