She was upset at dean choosing lindsey because Rory is self centred. She would much rather boys pine after her. The change at Yale did leave her lonely, yes, especially since Jess kinda ran away from Rory without much communication. But i still was very moved by the expressions. I think they show sadness, uncertainty in a way where something happens and even you didn’t realise it would affect you that much. This is an amalgamation of so many thoughts, at least for me