Memory is a bit fuzzy, but didn't Rowling say/strongly hint from the start that Harry is going to be a great wizard, and then spent 6 books showing (as opposed to explaining) how and why?
I prefer the theory that they knew all along that Neville was the chosen one. From Cracked.com:
"Basically, that Harry Potter dude was just a distraction. The "chosen one" was Neville all along. See, the plot of all seven books revolves around the idea that Harry's life fulfills this prophecy:
The one with the power to vanquish the Dark Lord [Voldemort] approaches ... born to those who have thrice defied him, born as the seventh month dies ... and the Dark Lord will mark him as his equal, but he will have power the Dark Lord knows not ...
The thing is,
all that stuff applies to Neville, too. His parents had thrice defied Voldemort, and he was born on July 30, one day before Harry. So what power does Neville know that Voldemort doesn't? According to the theory, that could be either "the power of love" (as in Harry's case) or
"herbology."
The "Voldemort will mark him as his equal" part was a little trickier, but then again it wasn't clear how it related to Harry, either. Neville had a messed up relationship with his parents, mainly due to the fact that Voldemort had them tortured into insanity. Voldemort had some serious mommy issues, too, so in that sense Voldemort made him his equal.
But the best part of the theory, the part that makes it all come together, is the idea that Dumbledore, the principal of Wizard High, was intentionally allowing Voldemort to think Harry was the chosen one
just to protect Neville. While we're not saying they should have just ditched Harry in the last book and turned the other kid into the protagonist, it
would have been pretty cool to have Harry find out he wasn't the center of the universe after all, if only because it would have made the character slightly less insufferable."