The order of the timeline is as follows: Generation I/Generation III -> Generation II/Generation IV -> Black/White -> Black 2/White 2/X/Y
The timeline works as you'd expect for the most part but it is nice to know where Pokémon X and Pokémon Y fit into things and that they do indeed come after the stories that take place in Unova. Toshinobu didn't state how much time had passed between each generation, but we know from the games themselves that three years passed between the first generation games and generation two. We also know that two years pass between Pokémon Black and Pokémon White and the events of Pokémon Black 2 and Pokémon White 2.
This leaves us with quite an interesting situation in regards to Pokémon Omega Ruby and Pokémon Alpha Sapphire. If the games are direct remakes that places them right back at the beginning of the timeline, which is certainly an interesting idea when so many stories have come since the original Pokémon Ruby and Pokémon Sapphire. Guess we'll see what happens when we learn more about the new games!