I think Yahtzee summed up the main problem with Portal 2 as well: It sets out to tell the story more in depth at just the point where the story stops being interesting. It also hits the reset button on the perfectly satisfying ending of the first game, at least for the main character, in what is known as a “Men in Black II dick move”*. I really think Portal 2 should have had a brand new setting away from the facility and a new main character. Surely there must be other cool environments that could do with some portal technology to shake things up.
*(It’s not? It is now!)