The chances are exactly 50-50, but that doesn't mean it'll alernate years: in the long tradition of the event there will be spans of several years where the #3 has been in the #2 half every time, or otherwise. Past results have no meaning on this years result.
Obviously Nadal fans don't want Djokovic on Rafa's side of the draw and risking Madrid happening again, Djokovic will want to be on Federer's side of the draw to avoid Nadal and have a better chance of reaching the final. Federer, I suspect, doesn't mind too much: on the one hand his chances of winning increase with Djoko on Nadal's side, but on the other I'm sure he wants to prove he's better than Djoko on clay and would love to do so by beating Djokovic in the semis. Murray, obviously would prefer to be on Federer's side of the draw, not that he could reach the final anyway, he'll be happy ( or should be) if he reaches the last 8.