I'm not sure if Portal 2 is a great example for a great videogame story. It's hilarious, sure, but I'd imagine there would be quite a few examples you could have picked that are better in that regard.
Planescape: Torment comes to mind almost immediately as a good example as well. IMO if you think all the stories are the same and are all bad you haven't played enough RPGs, or at the very least you've been getting rather unlucky with the titles you're choosing.