I think there is one scene for everyone that has touched a nerve, and that was the final straw of our hatred for the SE. For me it was Hayden inserted into ROTJ. I absolutely hate it, it is such an insult to every fan who grew up with it, cause it makes the PT infest the OT, when Lucas should have written the stories the other way around.
If these changes for never made, for me, I would probably be fine with the SE:
Star Wars-
Greedo shooting first
When they approach Mos Eisley, the jawa hanging and swinging (it is so childish)
Jabba insertion scene
When Han is running after the stormtroopers and before he saw 5 of them as he suprised, now there is a whole room of them!
ESB
The Wampa screaming after his arm got cut off
Vader going to his shuttle in Cloud City
The new Emperor scene with Ian McDiarmid
ROTJ
The new song in Jabbas Palace that sounds like an MTV Video from the 80's
Boba Fett flirting with the women aliens, come on now George!
Putting the gungans and every city in at the end of the celebration, taken focus away from the characters
Hayden as Anakins Ghost
If they were purely cosmetic changes, I probably wouldn't be complaining too much.