On the exra's of Episode III (the same documentary I got the screen shot at the beginning of this thread) he admits to the fact that in Epsiode IV Darth Vader was nothing more than "just a villain". In Episode V he hinted on a possibility of a father-son relationship between Luke and Vader, but at the beginning of writing for Episode VI he still had serious doubts if he would continue along that direction. Words along these lines are spoken by George Lucas in an Epsiode VI 'making of' documentary I have on VHS.

With all this in mind I believe there may have been a rough outline to the story which spans more than just the movie that was made first, but never in the sense that would make Vader's (or Anakin's) role more prominent or central to the Star Wars 'mythology'. In Epsiode IV Vader is nothing more than a henchman to Tarkin (which places him lower in the Emperial hierarchy) than Tarkin, but in Episode III he's the second in command to the Emperor.

Are these (amongst many others) the kind of plot holes and continuity errors that need to be addressed while re-working the OT en PT for the 30th Anniversary release in 2007?

The Original Trilogy stories are OK just as they were when they were released to the public. But George Lucas messed up while writing the Prequels, neglecting important character releationships, timelines, etcetera that had been established in the Original Trilogy for years.
Ever since the Original Trilogy the Star Wars 'universe' has been expanded by the publication of Star Wars games and books. For all of these additions to the Star Wars storyline (I assume) George Lucas has kept a watchfull eye. After all, any license the the Star Wars franchise has to go through George (or his company). However voluminous the Star Wars universe may have become over the years, he should have taken all of these additions into account while creating another part of the story or filming Episode I to III. Apologies NOT accepted, captain Needa.

As far is comparing Lucas' writing to Tolkien's work ...
Tolkien wrote The Hobbit first and The Lord Of The Rings after that. The chronology of the story line is simular to the publication order of the books. Hobbit first, The Fellowship Of The Ring second, The Two Towers third and finally The Return Of The King.
Tolkien's The Silmarillion however was published much later. Tolkien died before he could finish it, his son Christopher completed it based on his father's notes and existing material written earlier. The Silmarillion documents all the back story to the events in The Hobbit and The Lord Of The Rings (and other stories). A sort of Middel-Earth 'bible'.
In that respect the Prequels are a sort of 'mini' The Silmarillion, just focussing on a very small part of the Star Wars backstory.