The episode numbers will stay the same as there will still be 3 prequels.

I'm not sure why many people think that Yoda has gone nuts when we first see him in ESB (since the prequels came out of course). He is just acting like a strange creature, testing Luke. You see the disappointment on Yodas face when Luke says that he couldn't help him find his "friend". If he acted his true self then Luke may have realised that he was in fact the person he was sent to find.

There never really was a surprise that It was Yoda, even back in 1980. The revelation is in place for Luke and not the audience. So the prequels haven't ruined that revelation, luckily.

The whole Vader thing on the other hand is going to be a tricky one. There is no way of changing the fact that Obi-Wan lied to Luke about who killed his father and ROTJ sort of explains that anyway, even though it's pretty lame. But you can keep the whole "father " revelation a surprise and still keep the final duel in ROTS. I have a few ideas about how to keep the fact that it is Anakin who is Vader that can be pulled off, and in fact someone has come pretty close already to how i'm going to do this. I do have a lot of the PT already mapped out and quite a few different ways to accomplish things, which is why i will have to do all 3 films together. If i did them in order, one at a time, and something i had planned for ROTS didn't work, but there had already been something mentioned or built up in one of the earlier films, then it would be a complete disaster. This way, if this happens, i can go back and change something well before the films are released.