The only reason I can think for that would be that his ROTS outfit would have been too dark.They superimposed his head on Shaw's body. Can't believe Lucas would go through all that effort while he could have just filmed Hayden full body with his actual outfit and it probably would have looked much better.
Although it seems that if he was wearing his cloak it wouldn't look bad. For that matter, they could gave gone with the somewhat lighter AOTC outfit but a regular Jedi cloak. I say this will full knowledge of the heads that would explode to see ROTS Anakin (hair) in AOTC clothing.
What would have been cool would be when Anakin appears, have him raise his hands slightly in amazement, showing us that they're no longer bionic, showing us the extent of his transformation.