Rory's relationship to Logan can be much like Lorelai's relationship to Christopher while her relationship to Jess was more like her own with her dad, in the sense that he kept coming in and out of her life.

That Jess part right there just blew my mind. Oh my goodness, I feel like I'm suddenly looking at GG with brand new prescription lenses. And you're right, it totally explains the Dean thing, too!

I'm going to go sit in a corner and stare at the wall now haha.