In my opinion, people who write off literati's relationship as "toxic", or reduce it to an inability to reach depth in 3 months don't know how to read writing and feel uncomfortable to not seeing things as black and white.
Rory's unconfirmed phone call with him where she says, "I love you", and lets it go is an exhibition to their entire relationship. It's unfinished. Rory obviously still loves Jess, and if we really got into it we could talk about how Rory jumping into an affair with Dean is partially about Jess, but I won't veer off into that topic iykyk. The status of the connection between them is uncertain....the way their entire knowing each other has been. Jess and Rory's meeting started a domino effect that caused curiosity and was inevitable. It's not problematic on their characters or reduced to unforgivable readings on their integrity and moral attributes; they were 16 and didn't know themselves beyond what's predictable to the happenings of their life. Rory's best friend is her mom (also Lane) and even she can't understand Rory to her core at times. We could talk about how Lorelai often pressures Rory to who she wants her to be and overly influences her identity, but some people aren't ready for that conversation. Jess gets her, and vice versa; there's and understanding that's unspoken; there's an unveiling to secret parts of their personality.
The whole point of Jess fighting to gain Rory's affection and then flubbing it very quickly into the relationship is 100% intentional and I hate when people write it off as choppy writing or use it as a character flaw....forgoing his trauma-history with running, commitment issues, and going on to disappoint people because of his lack of self-esteem or belief he's worthy of happiness, understanding, and love, especially with Rory. They weren't supposed to date for a long time, or run off into the sunset. Jess was supposed to be a bad boyfriend because the lead up followed by his failings is the wasted potential to something grand that results in a separate trajectory to his personal growth.
Their relationship's unfinished in the way they were obviously headed towards saying, I love you (but didn't); it's unfinished and meaningful in the way Jess likely would've been Rory's first before all blew up from their poor communication the night of the hockey game to him not graduating to Kyle's party brawl. Jess and Rory aren't meant to be a healthy teenage romance. That's part of the appeal of their romance. They're individually complicated, they're parallels, they always find each other through time and space. They always cross paths and it's never really over. They could be the lost loves of each other's lives or (and the more likely scenario) like Lorelai and Luke...two people who consistly kept missing each other, weren't ready for one another, or can find the right time to collide. That's what makes them likeable to fans. It's not perfect, but it's a special bond and it's always connected. It's meaningful because it's deep, and the show gives many proofs to back this timeline course for reuniting. Jess and Rory are the endgame and they're complexly layered to incite interest.