I'm overall happy with the ending, and I pretty much have been since my first viewing. The very last scene kind of reminded me of the last moments of Phantasm II, which is always a good thing.
That said, I do have a couple of gripes, probably shared with others.
1) Audrey. Although I've found myself flip-flopping on this, I still mostly wish that Audrey had more to do. Originally, I wished she had a scene after her "wake up" scene, but I've kind of come around to that being a cool enough ending for her character. She wasn't really important in the latter half of season 2, so I've come to accept that she was relegated to unconnected side story status. With that said, I wish that maybe her appearances were spread more throughout the season, or that there were a few of them in the first half. I dunno--I guess it fits with how the other "unimportant" TP characters were dealt with. They all got arcs across 3-4 episodes or so, generally in episodes grouped pretty closely together. Maybe this complaint isn't so much about Audrey as it is about these characters felt like afterthoughts kept around for old TP flavor.
2) I think we needed one more meaty Sarah Palmer scene. Maybe even just an extended take of her smashing Laura's picture with her maybe doing something else "lodgey." This is ultimately forgivable since the final scene plays with the expectation of encountering Sarah again, but really, Grace Zabriskie has been amazing and I wanted to see her chew on some scenery one last time.
2a) Maybe an unfair bitching point, but I really wish Ray Wise had more than one scene in The Return.
3) I'm not terribly fond of the Judy-related retcon-y info Gordon is describing at the beginning of 17. I know it at least jives with FWWM, but I'm not sure if it does with the original series. Either way, it was an exposition dump that was really unnecessary to the plot at that point.
4) This totally could have been like 10 episodes. None of that Richard Horne stuff ended up being important. None of that Caleb Landry Whatever stuff ended up being important. None of the Shelly's daughter stuff ended up being important (we never even saw Shelly or Bobby's reaction to her apparent death--or even found out if she actually died). I'm forgiving of giving the old fan faves tossaway plots in order to score some nostalgia points and feels, but this season introduced a bunch of new characters that ended up not having a point or being entertaining, and then gave them more screen time than those old faves. I guess we at least got that awesome home invasion scene from Richard Horne.
5) I'm still unsure about the coordinates Mr. C wanted and what his goal was. Was he really looking for Judy, which seems like the most likely scenario given the white room sequence where the Giant changes the Palmer house to the police station as a trap. I know you shouldn't apply logic or thought to a Lynch story, but wouldn't Bob have noticed that he was living with Judy during that period that he killed Laura Palmer?
Overall, I loved the season, and I even liked the shaggy dogginess of a lot of it. It would just have been nicer if the dog was less shaggy in some areas and shaggier in others.