I can certainly understand why some don't like the fact that Begins doesn't "fit," however, I personally think it fits just fine. I look at the titles as a progression, which is why I think Begins fits in the flow from title to title to title. I made some lengthy posts on the day that the title was released, but essentially my reasoning is this:
BATMAN BEGINS - Batman, our hero, starts his crusade. At this point, he is just as his name says - a guy dressed up like a bat (clearly has issues

t

. This is the origin.
THE DARK KNIGHT - Bruce faces his greatest challenges yet, and by the end of the film, he falls. Our hero, Batman, has evolved into something much greater by the end of TDK. Attaining this status, he is Gotham's Dark Knight. Is he still "Batman?" Of course. But he now transcends the literal monicker, and takes on a new level of the symbolic status that he hoped to achieve ever since his training with Ra's. "He's not being a hero, he's being something more." As mentioned, this comes with a price, as the birth of the Dark Knight coincides with Batman's fall. In the grand scheme of the trilogy titles, a literal title (in the same realm as "Begins" and "Rises") for TDK really could have Birth of The Dark Knight, but that is indeed a mouthful; The Dark Knight fits the idea more elegantly.
THE DARK KNIGHT RISES - this one is obviously difficult to go into too much detail about (unless I'm Chris Nolan...), but a viable and possible idea is that now evolved yet fallen, the Knight must pick himself back up and "rise." He is no longer simply "Batman." Of course he still goes by the name, but thematically and symbolically, he is in a new place. That is why, although perhaps nicer to the tongue, Batman Rises would seem like a a bit of a step back to me (not to mention you'd get people saying that TDK now feels left out), but again, it's very hard for me to write this without considerable knowledge of where Rises is going, and how Nolan is ending his trilogy.
Unlike the "titles full circle" idea that many share, I see the three titles as a thematic
progression, with a beginning, an intermediate stage, and then a definitive ending. This is why I feel that Begins very much belongs. It leads into the Dark Knight, which then leads into Rises. Begins, (Evolves - moves past just the "Batman" title), Rises. After all, he's gotta be Batman before he can become the Dark Knight.
Just my opinion on the matter. I certainly don't wish to impose it on others, save for a few (just ALP). Kidding.

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