The fandom buzz around this issue comes in two waves: first, it seems that JKR has decided that Hermione and Ron shouldn't have ended up together; second, she appears to think Hermione and Harry should have. To the first accusation, I can't help but agree at least a little. There's a lot of dysfunction waiting to happen in that relationship. To the second, I can't agree at all--Hermione and Harry would drive each other batty at least as quickly as Hermione and Ron would.
The bigger question though is not about the Harry Potter-verse, but about the larger phenomenon being exhibited here. Do authors have regrets about where their stories ended up? I had never actually thought about this possibility before, especially not for an author like JKR who always seemed to have her books figured out. Particularly in light of how stories are twisted and manipulated for adaptations in plays, movies, and fanfic, I wonder how frequently authors think they made a mistake in their writing. Whether it's something relatively large--at least to a fandom--about pairing off your main characters, or something smaller (like whether Austen's Mr. Collins is tall and gawky or short and awkward), do you think authors often think their stories should be changed after it's already too late for the fans to get the memo?
The article that introduced me to this literary nightmare--http://ohnotheydidnt.livejournal.com/85367803.html
The Hypable article I'm only including because Andrew Sims used to be THE MuggleCaster and must feel similarly to me about this issue--http://www.hypable.com/2014/02/01/jk-rowling-ron-hermione-relationship-regret-interview/
The MuggleNet article that's a lot less reactionary than other sources--http://www.mugglenet.com/app/news/show/7697
"The Trio Harry Potter WD." The Quad. N.p., n.d. Web. 2 Feb. 2014.