I've personally never had a problem with the Chosen One prophecy. It's one of the few things that George didn't make a character explain in simple terms, but it makes perfect sense to me.
From my POV, Anakin DID bring balance to the Force, just as predicted. The problem is that the Jedi misinterpreted it. They thought "balance" meant peace and harmony, but by the time Vader was finished in EpIII, there was Yoda & Obi-Wan and Palpatine & Vader. It was a perfect balance of two-on-two. The misinterpretation could have been an interesting element to delve into more deeply, but like with many things in the PT, George just didn't bother.
What might be explored in the ST (though I doubt it), is that Luke created an imbalance when he was the only one left; it's only natural for more evil to come lurking to "balance" the Force again.
What do you think: interesting... or nonsense?