So the game takes place a bit after RBY/FRLG but still before GSC/HGSS, right?

Is Red going to be the Champion? Is Blue going to be the Viridian gym leader? How are they going to deal with Giovanni since he disappeared right after losing to Red (the Celebi/Silver event)?

Also the Rocket Hideout and Silph Co. puzzles are probably gone now that they're not part of the story anymore, right?