All the Episodes certainly need some tweaking to better flow as one whole movie. Some decent editing and some rescoring by John Williams would make a huge difference. Here's my 2 cents:
Episode I: The Phantom Menace
01. Restore the cut scene showing Qui-Gon destroying the Sith-probe in Mos Espa. It explains why Qui-Gon and Anakin are later running in the desert. That always bothered me.
02. I hope ILM really did replace the Gremlin Yoda puppet with CGI.
03. Maybe somehow add a scene that establishes Dooku as a malcontented Jedi with some concerns over current events. (It's probably too late to do this, but it would've been nice.)
04. Jar Jar didn't really offend me, but considering his non-importance in ROTS, I would trim his scenes a bit to make the fan majority happy. Too much screen time was given to a throw-away character.
05. If there's any cut footage showing more interaction between Anakin and Obi-Wan, I would restore it. Obi-Wan doubts Anakin throughout the entire film. But I wanted to see him reacting "amazed" by Anakin's Force abilities after his return from the Naboo space battle. It certainly would've clicked a little better with Obi-Wan's dialogue in ROTJ. (It's probably too late for this as well.)
Episode II: Attack of the Clones
01. Lucas says this is a love story, but he removed the subtle and classy romance scenes, while the ickier ones remain in the final edit! I would restore the three deleted scenes between the lovebirds on Naboo. All were acted quite well (better than the rest of their scenes together), and help to establish a genuine attraction between the two. And it's nice to see Padme express desire for a family life. Without these few touching moments, the viewer has a hard time understanding why Padme ever falls for Anakin. AND, I would cut out Anakin's thirty-second "It's not fair!!" tyraid in Padme's bedroom on Coruscant. His character comes across a hundred times less psychotic without this whiny little outburst.
02. Fix Qui-Gon's (ghost) voice. Liam Neeson says “Anakin…”, but that's not Liam’s voice shouting "Nooooo!!!" It's distracting for fans, and confusing to the casual viewer.
03. Redo the music editing. You can tell where scenes and music have been cut and reworked at the last minute. Also, way too much music was regurgitated from Episode I.
Episode III: Revenge of the Sith
01. I liked the Rebellion subplot, especially the scene with Palpy & Anakin. It's only a few extra minutes of footage, and it would certainly give Mrs. Skywalker something else to do besides crying and dying.
02. I'm part of the the club that desperately wanted to see (or at least hear) Qui-Gon's spirit on Polis Massa. I still want this probably more than everything else on this entire list combined.
03. I wouldn't mind the reinsertion of the Dagobah scene. It's not terribly important, but it's only 30 seconds long, and wouldn't hurt the film one bit.
Episode IV: A New Hope
01. I think we would all appreciate the subtle addition of the Imperial March theme in various scenes, at least for Darth Vader's first appearance in the film.
02. Perfect the lightsaber effects and remove the frame jumps during saber ignition. Also fix the new 2004 edition green saber problem.
03. Restore the original shooting scene between Han and Greedo. [I know this won't change, but a fan can dream.]
04. Perhaps add a scene of Bail Organa (and/or others on Alderaan) watching the Death Star enter their system.
05. The lightsaber duel definitely needs a tune-up in light of Ep. III. George can easily add stunt-doubles and/or CGI wide shots of Obi-Wan and Vader fighting like they mean it. Actually, Ewan and Hayden could even perform the fight. I bet they would each do it in a heartbeat if asked.
06. Perhaps a softer variation of the "Battle of the Heroes" theme can be added to the otherwise silent duel.
Episode V: The Empire Strikes Back
01. Restore Luke's line to Artoo, "You're lucky you don't taste very good".
02. Perhaps alter Vader's (Special Ed.) arrival in the Star Destroyer hangar bay so that it doesn't look so much like the hangar bay of the 2nd Death Star. And what's Moff Jerjerrod doing there anyway?
Episode VI: Return of the Jedi
01. Restore the minute- &-a-half of cut footage of Luke stashing his new lightsaber inside of R2-D2's dome. The music is really ominous for this scene. I think it would help give Luke a bit more of an edge.
02. Polish the CGI and bring back the original song (Lapti Nek) during the dance routine at Jabba's palace. [I know this will never change either.]
03. Digitally remove/replace Greeta -- her wrinkly green costume looks really fake.
04. Restore the deleted sandstorm scene. It's the only scene in the film shot with the full-scale Falcon set. I'm kinda sentimental about the Falcon.
05. Fix Han and Lando's crappy blue-screen scene (in front of the matte painting of the Falcon). Again... I wish they used the full-scale set.
06. Maybe finally Remove the black spot from the Emperor's face/hood.
07. Polish the final space battle so it looks at least as good as the Special Edition changes for the Battle of Yavin in ANH. The ships come across a bit flat (or 2D) in some places. I think this could've been done better even in 1983.
08. Fix Anakin's schlocky ghost appearance. Anakin's head nodding & smirk are a little disconcerting. I might be mistaken, but I think his face was cut-n-pasted from his "apology to Obi-Wan" scene in ROTS. That's kinda cheap. Anakin took a 24-year vacation from himself, but returned, and died at the age of 47. I would expect for him to appear 47 years old, not 23 (as he appeared when he became Vader), AND not 77 (as Sebastian Shaw appeared in the original version of ROTJ) either. The original scene certainly needed replacing, but it should have been done the right way. Lucas could either wait two decades to reshoot the scene with a middle aged Hayden (I'm joking), or he could double his age now with the help of state-of-the art make-up. It just doesn't look right seeing elderly Obi-Wan and young Anakin (with a bobbly head to boot).
That's all.