Originally posted by Time Immemorial
If Manhattan gets his power set the same as the real world. Then he is intangible, I don't know how he could copy him if Smith cannot touch him.
He wasn't intangible as far as I recall. Not that it matters because if he's in the Matrix then he's expressed by code which in turn is governed by the programs of the Matrix. The same programs Smith had taken control of at the end of the movie, hence his ability to redesign the Matrix in its entirety.
There are no whats, ifs or buts about it. Smith would win.