I've personally never had issues with the plot of ROTJ. I always thought it tied things up nicely, which is exactly what it was meant to do. Aside from its lighter moments and lack of death, ROTJ has a very heavy weight to it.

Removing some of the sillier elements like the dance number in Jabba's palace, and some of the droids banter would be a good start. Additionally, making Endor the wookie home planet would have led to a much more effective ground battle. Having enslaved wookies breaking free and join in battle with the rebels would be awesome. It would also make the motivations of Han and Chewie far more meaningful.

Aside from these types of superficial flaws, there isn't really much else I would change. I personally liked the fact that the first half hour is completely unrelated to the rest of the movie, and that Leia ended up being Luke's sister, etc...

Hindsight is always 20/20, but I've never put much thought into what I would have done if given a blank slate. These are just the issues I have with the existing film.