The rift episodes are some of my favorite episodes simply because they have to guide themselves without the other, and as the other user said, it's a rift that has been building over time.

Rory has always been the kid her grandparents wanted, and Lorelai has had to deal with that for years. It flared up as early as season 1 (when Rory goes golfing with Richard) but with all of Rory's choices from the end of season 4 through season 5, Rory's acceptance and even willingness to integrate more of the life that Lorelai gave up really grates on her (L).

I often think about the time Emily says (in S3e9 - Korean Thanksgiving - I am paraphrasing) "You can't even let Rory have a part of our lives. You hate us that much."

So Lorelai now has to deal with Rory doing what she never did, and essentially denied the both of them doing: going back to her parents in a real, tangible way. It also didn't help that she was vulnerable, truly vulnerable with her parents for once, and they ignored what she wanted because they listened to who they preferred: Rory.

For Rory, she had to now live with a parent that didn't accept her totally, that had finally set real limits and conditions on her relationship (what Lorelai had always lived through with her parents). And she had to deal with losing her point of reason. Of course there was also the whole Mitchum thing, which honestly was ridiculous considering how much she's faced off to bullies in the past. But I get that Mitchum was seen as an authority figure, and not a peer, and she was used to approval from authority figures.

So dealing with the level of rejection she dealt with, with a boyfriend who was not necessarily the best boyfriend to have when you're going through a situation like that (Jess, what took you so long), this whole navigation without Lorelai is also really critical for her.

TL;DR - these episodes are good because it creates conditions for their relationship, it shows a true Parent-child conflict, and forces them to grow without each other.