There are two worlds of physical ability, which will come into play. Romo, who may be medically cleared to play, but he no longer has the physical ability to escape that he used too. He'll take the sack or get run down for a loss versus Prescott, who has the ability to escape, make a play with his legs, and who has the confidence of the team. The argument that Romo is a better thrower is getting harder to make. Prescott vs Washington produced a 73% completion percentage, with no interceptions, and almost 300 yards. He completed passes to 8 different receivers and lead the team to 27 points. His QBR rating jumped from # 11 in week 1 to #4 in week 2.
It's going to get ugly when Romo comes back, looks rusty, and for ego reasons, Dallas can't take him out of the game.