I don't think things like the Darth Vader TPM poster indicates that they were not meant to be seen as true prequels. It was obviously used to market it to people who were familar with the old films. From a marketing standpoint, it would be unreasonable not to try to invoke nastalgia in such ways. Vader breathing at the end of the credits was not much more than an easter egg, a treat to the fans. "I have a feeling you'll be the death of me" was an in joke. And the ROTS ad calling it the end of the saga was again, marketing to the original audience, and indicating the fact that is was the last movie in the saga to be made.
I get what you are saying, and agree. The poor PT seems to suffer from some pretty harsh identity confusion, "Am I the beginning? Am I the end? I am so confused? What am I? I must be some kind of a freak!" (yup!)
I think all the things you mentioned were inevitable symtoms of being a series of prequels made 20+ years after their sequels. The actual features themselves, despite being clever enough to reference the older films in "cute" little ways ("I've got a bad feeling about this", "you'll be the death of me", and so on), seem to be striving to be true prequels.
It is George's complete lack of creativity that makes them seem as if they are made to be views with part one following six. With some creativity he could have found ways to make Anakin's turn convincing, to keep the "I am your father", "Leia is my sister" surprises intact for future generations. Just a modicum of creativity is all it would have taken, but the old man is spent, he's got nothing left. He has been demostraiting that to us again and again since 1999. Instead of even trying, he gives up and says that it was impossible.
George, who was the primary creative force behind the PT claims that they are meant to be seen before the others. His intention was to make them all fit together as a series to be seen chronologically. He just couldn't to it.
As a result of his miserable failings, mixed with nostalgia targeted advertising and a few in jokes, and you have a very good reason to believe they were intended to be seen in the order in which they were made.
At least, that is my perspective on it. Though I have to concede, they work much better as companions to the OT, non-canonical extra features intended to be seen after the main features, meant to give viewers an idea of what might have happened in those years before the rise of the Empire and the near extinction of the Jedi. Somehow, I have a feeling George and I would fail to see eye to eye on this though.