The National Dex can be obtained from Professor Oak at Olivine Harbor after defeating the Elite 4.
Once you defeat Red (who's still at Mt. Silver), you can obtain a Kanto starter from Professor Oak at his lab, and a Hoenn starter from Steven at Silph Co.
Steven also tells you Latios is roaming Kanto, for whatever reason.
Cinnabar has still erupted, haha.
Mewtwo can now be found in Cerulean Cave!
Zapdos is outside the front of the Power Plant this time. Moltres is in Mt. Silver, and it looks like you have to use Rock Climb to get to it. Articuno is still residing inside the Seafoam Islands.
Blaine is also still at the Islands, although this time he's acquired Gym trainers and the "Gym" isn't just the inside of a cave anymore.
That's all the interesting stuff for now; if you want more info, go to Serebii.Net's
info page.