I think the game with Chell is over.
It was fun, but it's time to let her go.
EDIT: Chell isn't a character, at heart.
She has no personality other than the one assigned to her by the player.
What will she do after Portal 2?
I'm sure some gamers would have her continue away from Aperture, independent and free.
I'm equally sure others would feel an emotional bond to GLaDoS, and have Chell return to a Rattman-like existance within the walls of the facility.
Some gamers might harbor resentment toward GLaDoS, and wish that Chell's freedom is false, to further justify their feelings.
Valve can't choose one without alienating other players.
EDIT, AGAIN: Maybe a moral choice system could be implemented?
Personally, I'd like to see Wheatley return. Yes, he's in space. But put yourself in his shoes.
You are small, insignificant, and confined to a rail for CENTURIES.
You've been given plenty of cool equipment, but told that using it would result in death.
You are powerless, living in fear.
Finally, you make a bid for freedom, waking Chell up and asking for her help.
Even in your escape, you still have to depend heavily on her.
She figures out how to disable the neurotoxin and the turrets, and even with your hacking skills you can't help feeling worthless.
Then you gain control. GLaDoS, the overlord, has swapped positions with you.
For the first time in your life, you have a voice. You are strong.
Drunk with power, you revel in your newfound abilities.
Then your programming starts in. Your addiction to power is compounded by a testing addiction.
Even though, at heart, you are still basically good, this new addiction overcomes your basic nature.
You even try to kill the woman who carried you, when you were small and helpless, just to retain your powers.
Then it all goes wrong. History repeats itself a third time, and the overlord is overthrown.
You are banished to space, where you are REALLY helpless, to drift among the cosmos forever, pondering your own decisions. It's worse than being on a rail, really.
I hold that Wheatley deserves a second chance.
Personally, if I were god, I'd make him into a testing robot, like Atlas.
He'd have power, but not absolute power.
Because nobody deserves an eternity with a homesick Space Core.
But Portal 3 could be a good game, if it followed the humans awakened at the end of the co-op campaign. It could take on a survival aspect, maybe?
Or maybe a game set in the past, watching Aperture Science turn from the innovators of tomorrow (testing astronauts and Olympians) into a hopelessly crumbling corporation (testing hobos and tramps)
I found Cave Johnson's transformation from a hearty, take-no-prisoners juggernaut into a sickly, broken man one of the most intriguing parts of Portal 2.
Listen to the Lemon Speech, for example.
Comic nature aside, this is a once-powerful man now unable to stop the poisons in his bloodstream.
If you listen carefully, his voice breaks, slightly, as he says "Do you know who I am?"
He's being killed by something beyond his control, probably the only thing in his life he doesn't dominate. It's a fascinating irony.