EMILY: Christopher gets his life together with that woman.
LORELAI: So, that’s good.
EMILY: It should’ve been you!
Emily is extremely upset when Rory doesn’t come to Friday Night Dinner because she’s having a night out with Sherry. She immediately fears that Sherry will “take Rory away” from them, and is terrified that Christopher and Sherry will obtain weekend custody of Rory. She’s slightly on the old side to be a tug-of-love child at seventeen, and I’m pretty sure you have to pay child support to get even part-time custody of your child, which Christopher has never done.
Emily says she is heartbroken, because she always pictured Lorelai and Christopher being together, so that Rory could finally have two parents. Christopher was never ready to commit and was no kind of provider, but now it looks as if he was capable of settling down and working at a steady job, he just needed to find the right woman.
Completely and cruelly unfairly, Emily now blames Christopher’s general uselessness on Lorelai, saying that if she’d really tried, she could have influenced him to become a better man. Really? At the age of only sixteen, frightened, pregnant, and alone, she should have been responsible for Christopher’s life as well? Lorelai had a baby to care for and support, she didn’t need to take care of Christopher as well (and Rory would have suffered horribly if she did).
Emily is no better than Straub, laying all the responsibility for Christopher’s failure at Lorelai’s feet. It’s a horrible thing to say to her daughter.
Lorelai does admit that she has feelings for Christopher and isn’t happy about Sherry either, but she is trying to focus on doing what’s right, and being happy for Christopher. This unselfishness is roundly condemned by Emily, who goes upstairs to cry on her bed. (Later we find out she did eventually come down to dinner, but sulked all the way through it).
The episode’s title comes from Emily’s outburst to Lorelai, that, “It should’ve been you!”. Note that Emily’s outfit is mostly sad black, with touches of angry red. Lorelai is in grey, trying to remain neutral.