I had a good friend (when we were 20 or so) who was a big Star Wars fan as well and he was shocked to hear that ESB was my favorite. RotJ was his. I brought up some of my misgivings with it, and he said, "Yeah, well what about the 3-way battle at the end?" I had to admit it was pretty good... but still not enough to bring the whole movie up to the level of ESB.
Years later, I saw Revenge of the Sith. I had strongly disliked (violently hated, really) Episodes 1 and 2 upon first and subsequent viewings. The trailer for RotS made it look like maybe ol' George had learned his lesson and changed his stripes (again!). So I went into the movie with guarded optimism. That optimism was severly wounded about 5 minutes in when a pretty decent battle scene de-evolved into robotic mickey mouses crawling over Anakin's and Obiwan's ships.
After the scene where (SPOILER ALERT FROM 2004) Anakin kills Dooku, I thought: Interesting comparisons to The Emperor's Throne Room in RotJ. During the scene where Anakin is racing back to Palpatine's office, I thought: Oooohhh this could be getting good. It felt like when you sit on an old rollercoaster and it starts to slowly climb to the top. It's actualy slow and uneventful, but it fills you with excitement for the ride that's about to start. But then during what can only be called "the turn scene" I felt like the rollercoaster had crested the top, descened about four feet and then leveled off. Then we asked to politely leave the ride.
After the movie, my wife and I were discussing our relative dissatisfactions with the movie and specifically the "turn." She asked me how it could have been better. My mind instantly went back to the Emperor's Throne Room. It gave me an all new appreciation for how good that scene really was. When Luke uses the Dark Side while putting the smack down on Vader... that feels very real, believable and... smooth. It comes from the characters. Luke using the Dark Side something that comes from the character, something that's been under the surface the entire movie. Anakin's turn is something dictated by the script.
So, I've come a long way in my appreciation for RotJ. It was the most exciting to me as a young boy. Leia in that bikini was good to me as a slightly older boy. When school mates would talk to me about Star Wars, and they would ask me: "Which one has the teddy bears in it? That's my favorite!" I knew there was something off about RotJ. But it has the best (nay, only) ship-to-ship battle in the series and it has an ending that is not only competent, but actually satisfactory. And how many series can you think of that actually have a satisfactory ending? The endings either suck, or the once great series begins to slip into ridiculousness or complete craptitude. RotJ is great (my opinion of course), but it still had the fingerprint of "the begining of the end" on it.