On a personal note, I found that Advent Children in particular confirmed one thing for me: Jenova was the real villain, and Sephiroth was just being her bitch.
Despite the creators explicitly stating the opposite?

Charcoal, you can't simply ignore a retcon because you don't like it. That really is what this all boils down to. If the creators want to change their work, than it's changed. Same as with Star Wars and the Special Editions.