Since we are just over ten days away from the "Gilmore Girls" revival, let's just put an end to this whole Jess versus Logan debate, shall we? Here's a few reasons why Rory should have just stayed with Jess.
And for all of you Dean lovers out there...why?! He really was the worst.
Recommended for you
He challenged her.
Jess pushed Rory outside of her Type-A, straight-A, do-good box. He challenged her need to always be prim and always be right.
Jess was sassy.
And who doesn't love that? Witty banter always keeps things interesting. 
He's a man of his word.
He's loyal, he works hard (moreso outside of school), and he keeps his word, even if it takes him a little while, like paying Luke back.
Books!
Jess and Rory always shared a love of books with each other. He may not have worked hard in school, but he was well read and kept up with Rory intellectually; even questioning her disliking of Hemingway. I mean come on Rory; it's Hemingway!
Furthermore, he even wrote a book! So sweet. You know that this stemmed from his love of Rory. He even told her he couldn't have done it without her. I'm sure he realized how much it connected them thus he thrust himself into the literary world as much as he could. He even ends up owning an independent bookstore.
Jess is to Rory as Luke is to Lorelai.
I mean Jess is Luke's nephew and everything, so there is that obvious connection, but they both adore the Gilmores and manage to show it in their own quirky, endearing, perfectly Jess and Luke ways.
All of the little things...
Remember the time Jess outbid Dean for the basket, or the time he shielded her from a leaky roof with an umbrella, his silly magic tricks, his notes to her in the margins of her books, the care package from "Luke," the time they kept turning right, and how he knew the exact distance to Yale? 
Rory and Jess just understood each other.
They came from similar backgrounds that just happened to lead to different personalities that ended up meshing so well. Jess' daddy issues made him the rebel and Rory's made her a perfectionist, but they understood where each was coming from and challenged each other in the most perfect ways.
He wants what's best for her.
Jess isn't afraid to call Rory out when she needs it like when he comes back in Season 6 and he explicitly tells her "I know you better than anyone else. This isn't you." Well, he's not wrong. Get your butt back to Yale, Rory! 
They never actually say goodbye.
That has to mean something right?! Yes, there are times when he just leaves and literally says nothing, which is awful, but as they get older he just keeps coming back to check in. It's sweet, really; but in the end they still never say goodbye. Jess leaves Rory with, "It is what it is you and me." Is there really a better way to describe the two of them? Not really.
So, maybe, just maybe, Rory will get her act together in the revival and make things work with Jess finally. One can dream anyway.
