PARIS: So, that’s how you look when you’ve just woken up?
RORY: Um, yeah.
PARIS: Nothing in my life is fair.
Of course, the viewer knows that this isn’t how Rory looks when she first wakes up. Lorelai warned her the Puffs would be coming over, and told her to put on cute pyjamas, brush her hair, and wear lip gloss. Instead of going to bed, she stays up reading, then quickly jumps into bed when she hears the Puffs at the door, so she hasn’t even been asleep, let alone woken up.
Liza Weil is attractive, so they had to work quite hard to make her look frumpy for these scenes, including putting on a skin treatment which she obviously didn’t need. She still ends up looking pretty cute.