If I can the thing that I changed was the fact of April appear on Luke's life, all was OK when she appears, but then Luke told Lorelai to not get involved with April and to kind of not participate in that part of his life, but this part of his life get stronger and stronger and we see Luke being father almost 24 hours a day, and in that 24 hours Lorelai was in a second plan...and that destroyed their relationship.
Common I think April is a fine kid and all, but she mess up the ending, the relationship...
And I would change the relationship beetween Luke and Lorelai in season 6 . I would change the one thing that Lorelai ignore and that hurt her so much, the way that Luke push her away from his life, is so stupid and she just kept her mouth shut everyday until she don't take it anymore.