Logan was smarter than Rory
Everyone says that they love Jess for Rory because he could intellectually match her, but Logan could not only match her but even know more than her. He grew up in a very intelligent family, and in a lot of episodes we could see how he corrects her and challenges her. He makes her grow.
One of the many examples is on the episode “You jump, I jump, Jack”, when she says that she is a journalist and journalists don’t get involved, and he gives her a plethora of examples of journalists who did get involved to prove that her argument was wrong. Then he procedes to challenge her and say that she looked a little sheltered, which she was. Everyone else expected Rory to be or do “what she was” or what “she was supposed” to do or become, Logan was the only one who saw the multifaceted versions of her (even the not so good ones) and at the same time challenged her to become more.