I'm someone who grew up on the 1997 cuts, so while I prefer the OOT on the whole, there are a handful of things from the SE that I'd include if I were making a master cut for myself.
What I like from the SEs:
-The inclusion of the 1981 "A New Hope" crawl
-Fixing Vader's lightsaber after the duel with Obi-Wan
-Replaced shots of the Sandcrawler and Ben's hut
-Cleaned-up landspeeder effects
-Biggs before the Battle of Yavin
-Victory Celebration at the end of Jedi (I know I'm being a bad purist, but I've always hated Yub Nub. And I mean the 1997 version, without Naboo or Hayden)
Things I'm not crazy about but that don't ruin it for me:
-CGI in the Battle of Yavin
-the extended Wampa sequence
-Extended Cloud City approach
-Oolah in the Rancor pit
-Sarlacc beak
Things that aren't the absolute worst, but that I'd leave out without thinking twice if I were making the decisions:
-CGI dewbacks
-Mos Eisley approach
-Windows on Cloud City
-"Alert my Star Destroyer to prepare for my arrival"/other useless dialogue changes
-Anakin's eyebrows
Things that 200% need to go:
-Greedo shooting
-Jabba in ANH
-Ian McDiarmid in ESB
-Temeura Morrison's voice
-Jabba's ridiculous big door
-The dug in Jabba's palace
-"Jedi Rocks"
-Vader's big "NOOO" in ROTJ
-Gungans in the ROTJ celebration
-Ghost Hayden
As far as fixing compositing problems and bad mattes and the like, I actually prefer the cleaner "fixed" presentation. If the impossible dream of the OOT/SE branched version ever comes to fruition, I'd keep the stuff in my first section and then go OOT otherwise.