I never had a problem with the prophecy as such, there would have been no need to mention it in the OT as Obi-Wan and Yoda are spinning Luke a line for most of it and from Vader and Palpatine's point of view the Jedi were mistaken.
The only time it might have made some sense is when Palpatine is warning Vader that Luke could destroy them (thinking that maybe they got the surname right but not the first name).
If the rest of the prequel scripts had worked out fine it wouldn't have been such a stickler.
It ties in with traditional myths and legends and has a nice twist in there about the dangers of seeing just a little of the future without the full context (something else which occurs a lot in myths and legends).
If anything it would have explained why the Force is so strong in that particular family without losing the potential that with the right vocation and training anyone could become a Jedi.
The stupid Midichlorians however try and add a pseudo-scientific explanation for a mystical energy field which doesn't even make sense on a pseudo-scientific level (much like homeopathy).
I'm for all references to them being removed 100%.