KH3DS will take place in the same time frame as the rest of the Kingdom Hearts series. Beyond this, though, Nomura refused to go into further details on where within the body of the series the game lies.
You'll be playing as Sora and Riku, who will both be main characters. Different from Birth by Sleep, you'll be trading off between the two as you play. Switching between the two will be at the center of the gameplay systems, said Nomura.
Nomura plans on making use of the 3DS's 3D capabilities. He wouldn't go into details, but gave somewhat of a puzzling hint. As their means for using the depth of 3D, they're thinking about "falling." This, said Nomura, is something that people might have noticed in the game's E3 trailer.
Continuing with the mysterious responses, Nomura touched upon what he wants to do with Kingdom Hearts 3DS and the themes he hopes to convey. Regarding the things he wants to do, he said 'A KH you can touch, a falling Sora, and a flying Riku." Regarding themes, he said "Trust." More specifically, he said that the game will show how by trusting others, you achieve things that you just couldn't do on your own.