So what you have now is 1-3 as a character study of how Anakin is a little boy and turns to the darkside, which is very interesting, although could have been executed much better. Then we get to 4-6, and you don't really get that continuing story of Anakin Skywalker, because the OT movies weren't made with the tragedy of Anakin Skywalker in mind.
Episode IV has very little to do with Darth Vader, he is just some cool bad guy that kids like me in 1977 loved to death. All he is, is just a bad guy with about 15 minutes of screentime, so you have part 4 of The Tragedy of Anakin Skywalker, and the movie has very little to do with him.
Then you get to ESB, and the first hour again is dominated by the friendship of Han, Leia, and Luke to keep with the theme of ANH, or to anyone who forgets, the THEME OF THE OT before the PT. Cloud City gives the first hint of a bigger story between Luke/Vader with the revelation, but that is more of a plot point, not an overall character arc.
Finally you get to ROTJ, where again the first 40 minutes are dominated by saving Han, or showing that these friends will do anything for each other. The last hour is the only story that matches up with the PT as for the first time we see the inner thoughts of Vader as he begins to be conflicted around Luke, and isn't this bad ass anymore. That subtext worked perfectly when watching the OT in 1983, cause it wasn't the main theme of the trilogy back then, but a side story that added a bit of depth to the conflict of Luke/Vader.
So what has happened is Lucas is trying to marry a trilogy about Anakin 1-3 with a trilogy about Luke, and Leia & Han too, to make up the tragedy of Anakin Skywalker, and to me they are just two seperate stories when you try to watch them 1-6, not because of the quality of the PT, or the quality of the OT, only because they were written that way and Lucas changed the story before the PT.
The PT is just a backstory, and I can enjoy it as just that: information that fills in the blanks of the OT that I wondered since 1983. Now it is up to the viewer whether you view the PT as plot holes or plot holes free when seeing it as a backstory, but make no mistake it is not a linear story about the tragedy of Anakin Skywalker, cause if it was, Vader would be much more prevailent in the OT, especially ANH.