Maybe we can have two rather short story modes at the beginning of the game.
You can select whether to play girl or boy at the beginning and depending on your choice you'll see that part of the game.
Once you have played both stories (girl on the way to rescue, boy on the way to escape... and at the end they meet and now have to get rid of that dark divinity or so), you'll be able to play the main storyline, where the siblings have to cooperate (in their own stories you only have one character).

This basically is the "start with one, finish with two" idea, just separated into story. So the player gets the feeling to have unlocked sth.

This would allow to introduce both main concepts (time warp for the girl, gravity change for the boy - or vice versa) separately.
Also for the girl we could use some "warm" setting, while the boy is placed in some darker, creepy world, since he's escaping.
After having introduced both concepts, there's the possibility to mix up all the styles. Maybe like this: nice friendly past, dark, sad and scary future.