I don't think it is a writing flaw at all. People change their minds about things all of the time. It is certainly reasonable that she would have changed her mind after the choices were concrete. In the past, the college choice was abstract, she was not accepted to Harvard, Yale or any school. I am not convinced that she would do a pro/con list ahead of time, when it was all speculation. Rory (as a humble person) will likely not just have assumed that she would be accepted to colleges with such tough competition.
And I think this is such a great episode (top 5 of the series!). There are so many funny scenes.
Lorelai trying to be funny with the guests (and it not working)
Kirk's t-shirt "Faux Poes Foes" is funny on many levels.
Rory's puppet show
Paris watching soap Operas