Agreed on both couples. LL are my one of my OTP of OTPs, and to see them ruined like that in the last season -- or really the last two seasons -- was such a punch to the gut. I really blame the deterioration of their engagement to the introduction of April. It brought out the worst in both Luke and Lorelai's characters; one of Gilmore Girls only true jump-the-shark moments. I love LL to death, and am glad they reunited in the finale, but they never fully recovered from Aprilgate.
As for Rory/Logan, I am actually a Rory/Jess shipper first and forever, but I did grow to like RL quite a great deal, especially during my recent re-watch of season 6 and 7. I think the way they were written in the finale was total hogwash. Both of them acted totally OOC, especially Logan. The writers seriously wanted us to believe that Logan would propose to Rory in a room full of people and all her family? Seriously? Did not buy that. I also did not buy that he would propose to her at all, but let's suspend disbelief on that one and say that he could want to marry Rory at 22. Even if she said no, I don't think Logan is the kind of guy to pull the 'all or nothing' card on her, especially when marriage wasn't something they had ever seriously talked about. It's not like I was a huge cheerleader for an RL endgame, but in some ways I do believe Logan was really good for Rory, and I would have liked to see a better ending to their story.
In general the GG finale was a huge disappointment for me. It had some great Rory/Lorelai scenes, a Java Junkies endgame, a wonderful Lorelai/Emily moment, and a fitting ending for a just-graduated Rory. But I thought the writing of the main characters was not very consistent with the characters that AS-P created, and that was the worst blow to my fangirl self. I also wish it hadn't been so rushed, after seven years of build-up. But, oh well. I guess it's pretty tricky to create the perfect finale. I just wish they would get on making a movie in order to rectify that last season!