As for the changes... I was never sure I wanted to do them myself. I always like the subplot and it irked me it was removed... there's still another scene that was just Padme, Bail and Mothma talking... and it irks me that THAT'S not on the DVD...
What's worse is that ... it seems like they just kinda dumped the sturr on the DVD...
In the other dvd's, they FINISHED the deleted scenes and put them on the dvd... here, they mostly lay unfinished... which kinda annoys me.
As for the removal of Vader, I guess it was something that I was always unsure of...
The fan boy in everyone wanted to see Vader again... but going back and exploring the films and listening to the commentary and reading about the scenes and the inflections and what was going on... I have to say that I've gained a little more insight into what exactly Lucas wanted to capture and if there's one thing, the acting really did suffer in this film.
In the others, a lot of the problems with the acting I'm almost certain came from the fact that the films were re-edited soo much... it removed a lot of the acting and left strange leftovers of acting in parts that made no sense... like Anakin smiling in Episode II when he made Padme uncomfortable. Unless you've read the deleted scene, you don't understand why he should be smiling at all... and by all rights, he shouldn't be in the film edit because there was none of the humor of the filmed scene... but yet you see him smiling and it makes it really weird...
It's a bit annoying.
As far as Vader in this film... I think that removing it works for one big advantage...too much of the end of the film leaves you off where the next one starts... and in removing Vader, you also remove the Death Star... (you also remove the "Nooo!" lol)... you also remove Leia being brought to Alderan... (and since Yoda going to Dagobah is deleted anyways, you loose that as well).
What you're left with is a streamlined ending... that shows padme giving birth, dying, her funeral... and that takes you to Tatooine...and leaves Luke and Obi-Wan there... with none of the rest of that stuff...
It removes a lot of film time, and also alleviates a lot of the "Well, the next film starts right after this" feeling associated with it.
In a way, the deleted footage could almost be turned into another film itself... and in some ways should really be used as such... rather than as an ending sequence to Episode III.
A lot of them would be good to use either that way, or as flashbacks latter in the films... like in ROTJ... not to say I'm going to be doing that... lol but they make FAR more sense there than they do at the end of Episode III.