I disagree. Even without the Ultimania the theory is not at all strongly suggested by the game to be true. All the so-called "hints" used are very shaky, and if they don't have much more reasonable alternate explanations offered by the game itself, they simply don't stand strongly enough to constitute a plausible case. I believe the FAQ referred to shows this.

The thing with R=U, you see, is like you say; people think it's an attractive way of making the game better. So instead of starting with what the game tells us and inferring that R=U, people start with the conclusion that R=U and work backwards to try and show where it is implied. This is how ALL the 'hints' came to be, I can guarantee you. Unfortunately, this is very bad logic, and so the theory falls too short of being plausible. The Ultimania Guide was just the final nail in the coffin really...