At this point, you'd have to give them an equal shot to do well. They are both #2's on a decent offense. We know the Colts offense is better than they are showing right now, and they should break out of the doldrums in the coming weeks. They have some inferior teams coming up. The Colts did the same thing last year which is why they had such success in the pass game.
The question will be whether Manning gets the chance to throw TD passes or not. There's a lot of luck involved in play calling and outcomes, and last year was one of those deals where the optimal conditions existed for a huge season through the air.
I would still give a slight edge to Wayne at this point, but they are both looking like lower-end fantasy #2's at this point. At the beginning of the year, people were looking to Wayne as a #1 option.