Against the belief that writers didn't do their job well, if you watch the series again focusing on the Rory-Logan relationship you will find continuous proof that the final break up in season seven episode "Unto the breach" has actually been in the making very longly and since the beginnings of season six where the sudden touch-and-go return of Jess in episode "Let me hear your balalaikas ringing out" caused a big fight between Rory and Logan over issues regarding serious differences between them although they were inevitably bound.
After the fight, they don't see each other for quite a while and Jess' scolding has a positive effect on Rory, who comes back home to Lorelai and resumes her studies at Yale. Soon, Logan manages to get back with Rory, also with the unexpected help of Lorelai, who writes a mysterious letter we never know the content of. They briefly live an intense love relationship which starts fading abruptly when, in the episode "A Vineyard Valentine", Logan is forced by his father to accept a job in London by the end of his senior year at Yale. In the following episode "Bridesmaids Revisited" Rory goes to Honor's wedding preparations (Logan's sister) and she finds out by some of the bridesmaids that they have slept with Logan. Rory is hurt and decides to leave Logan immediately. The following episode "I'm OK, You're OK" Logan convinces Rory that he played around because he believed their story was over, while Rory just hoped it was in a stall. Their misunderstanding seems to don't matter anymore because Rory is willing to get back with him and stay at his house instead of Paris'. What happens next is that Logan starts understanding that Rory hasn't really forgiven him and in the episode "The Real Paul Anka" he decides to go with Colin, Finn and the Life and Death Brigade on a risky parachuting trip. At the same time, Rory receives an invitation by Jess at Truncheon Books, a small publishing house and art gallery that he founded in Philadelphia with a few friends. Rory goes to meet him and casually meets also Luke and April there because they are on a school trip. Jess tries to win Rory's heart back and they even kiss each other, but Rory feels that it isn't right for her. Jess lets her go for the last time, although he suggests her telling Logan about their kiss in case she wanted to obtain a final break-up and get back with him. Rory wants to be loyal and returns to Logan when he has a very serious accident during his parachuting trip. Rory will become his everyday assistant and their relationship becomes even deeper during Logan's convalescence. All up until the season six finale, where Logan, after graduating at Yale, is forced to leave America to go working in London for his father.
Season seven's first half is the long-distance chapter, where Rory and Logan grow more distant, both geographically and romantically. At one point, Logan comes back to New York to acquire an internet company and the two lovers meet with great pleasure. Rory finds herself irrationally jealous when Logan invites her at a dinner with two of his work-fellows and one of them, who is a nice girl named Bobbi. The jealousy seems to get them even more involved with each other. In the episode "French Twist" Rory meets two new friends, Lucy and Olivia, at an art exposition. Lucy's boyfriend happens to be Marty with whom she was friendly involved during freshman year and who was blatantly in love with her although she didn't allow him to go further because she was already involved with Logan. Right now the tables turn and Marty pretends he never knew her. This upsets Rory, who gets more unsettled in her relationship with Logan during the episode "Introducing Lorelai Planetarium", where she becomes charged up over Lorelai's decision to marry Christopher back in Paris without consulting her and over Logan when he feels offended by an article written by her on a pre-launch party organized by him yet full of snobs and people from the priviledged world she hates so much (like Lorelai). The couple fights badly and Logan replies Rory telling her that if she's still staying with him, maybe it's more about economic and residential stability. Rory can't handle Logan anymore and leaves their apartment telling him "Screw you, Logan". By the end of the episode, Rory understands that she must find a place of her own to gain more independence although she and Logan have managed to make peace again. She decides to go and stay at Paris and Doyle's new apartment.
During the following episodes, the problem with Marty returns and this time Logan will be involved. Rory confesses Logan that she's having problems with Marty because they were more than friends during freshman year and the guy simply prefered to pretend they didn't know each other when Lucy introduced him to Rory. Logan tells her that he's glad he told him and that he is not jealous at all, but when he, Rory, Marty and Lucy go at a dinner together, Logan turns the tables and tells Lucy that Rory and Marty knew each other very well. Lucy remains completely shocked and disappointed and leaves everyone. Rory becomes mad at Logan because what he did not only was obnoxious but also had the result of making her losing a friend and causing a couple to break up.
In the episode "To whom it may concern" Rory makes amends with Lucy thanks to Paris, but soon enough a new drama gains ground: Richard has a heart attack. During the hospitalization of him, Logan helps Rory like a true and caring boyfriend (in the meantime, Lorelai and Chris are distancing from each other because of Lorelai's remaining deep involvement with Luke). A few episodes later, Rory flirts with Richard's assistant at Yale and tells Logan immediately about this, confessing him she fears of having a self-destructive personality. Logan demonstrates that he understands her and in his opinion having discussed the matter already solved their problem. The couple is at a point where they believe they have reached a perfect harmony, but it's not as simple as that.... What will happen next is the most interesting turning point in the whole Rory-Logan plotline.
In the episode "I'm a Kayak, Hear Me Roar" Rory celebrates Logan's birthday big time, but at the end of the episode the guy receives bad news about a big failure at work. The following episodes, Logan becomes isolated from the world for a while and his father Mitchum, who basically is his boss, gets to him, trying to make him put everything back together. Logan doesn't want to do anything but relax at home and go with his friends partying (like he did back in college). Rory hates to agree with Mitchum but tells Logan that he must do something to get back on track. Logan goes to Vegas instead, without even inviting her. Rory returns to Stars Hollow to be at Lane's baby shower. Her issues with Logan are all still there, but she doesn't tell Lorelai directly also because she hates to admit it to herself.... But Lorelai guesses just by looking at her, she's her mother after all.
In the following episode "Gilmore Girls Only", Rory Lorelai and Emily go to Mia's wedding. There Logan surprises Rory and reveals her that he is no longer under his father and that he feels the world is opening up new doors to him. For a while, he goes living with Rory at her and Paris/Doyle's place. In the episode "Hay Bale Maze" he proves Lorelai that he isn't the spoiled and rich boy she always despised anymore. At the same time, Rory is taking in consideration many opportunities for what will happen after she will graduate. She tells Logan that among the factors in her usual pro-cons list she wants to factor him as well, but Logan suggests her to do what she feels she wants to do and then he will factor her in as well.
An emblematic moment foreshadowing that they will soon break up is when they get into the hay maze and at a crossroads Rory looks forward to go one way and Logan to another, they momentarily stop holding hands and then they go forward together but uncertain of the future.
The next episodes Rory takes a risk and applies for her dream: the New York Times internship. Unfortunately, while Paris receives multiple proposals from a lot of medical grad schools, Rory receives a negative letter from the New York Times that will put her very down at the point that she will be distracted at one of her literature final exams. Lorelai manages to bring back some hope to Rory's soul telling her that she can do whatever she wants and that she will never disappoint her. Logan gets a good job in Paloalto, California and tells Lorelai he wants to propose to Rory and bring her in California with him.
The second to the last episode "Unto the breach", Rory graduates and sees her horizons get wider no matter the New York Times internship declined her request (as a matter of fact, the next episode she gets a job as reporter during Obama's campaign). Things change completely when Logan proposes to her in front of a crowded reception room that the Gilmores are using to celebrate their grandaughter. Rory drags Logan away from the people and Logan tells her to take a risk like they did the first time they were really together (see episode "You jump, I jump, Jack"), but Rory really can't make up her mind, she can't jump this time and asks Lorelai to give her some good advice. Lorelai tells it's too big a decision to make it for her. Rory thinks of it overnight and after a long-awaited graduation ceremony where everyone (including Chris) is proud of her and teary, she tells Logan that she wants to pursue a career as much as him and that they could still be happy together trying the long distance method for a while... But Logan doesn't want to go backwards, he wants all or nothing. Rory insists that they should try long distance, but after finally uttering the words "What's the point?" Logan leaves her for good. Rory is sad and relieved at the same time, but she doesn't cry onscreen. During "Unto the breach" 's final scene, Lorelai discusses Rory's decision telling her that one day she will just meet the right person without any hesitation.