I would've liked more hints at Vader plotting against the Emperor. He seemed a bit defanged in Jedi and I like the idea of exploring part of the motivation for his search for Luke in Empire.

There was a subplot in rough drafts of Jedi about the Death Star's commander, Jerjerrod (read it in detail here). Basically the events of Empire caused the Emperor to lose faith in Vader, and he gives Jerjerrod the task of bringing Luke to him. He and Vader butt heads when Luke is captured, and Vader finally loses it and kills him.

I think there could've been a "breather" story between Empire and Jedi, similar to Shadows of the Empire. Luke would return to Dagobah to confront Ben and Yoda about Vader's revelation. The climax of this plot would be the Jabba's Palace part of Jedi. This would leave the next installment with more time to develop Luke and Vader.

I think the Empire could've been developed a bit more. Like in the show Avatar, where the more we see the villainous Fire Nation, the more we see that there are a lot of good people - they've just spent their whole lives living in a fascist state where they've been educated that their actions are for the greater good of the world.

I'll echo the need for more women in the OT. I was kinda bummed when I saw they cut female Rebel pilots from Jedi. I liked the shot of an older A-Wing pilot because it seemed like she had some story behind her.