Mueller “handed the Cohen matter over to the U.S. Attorney for the Southern District of New York, whose office is responsible for investigating and prosecuting FEDERAL cases in New York City.”
Which means that Pres. Trump still retains power and jurisdiction to pardon Cohen if and when he is ever accused or convicted of any Federal crimes. Moreover, it means that Pres. Trump has the ultimate authority to discipline anyone in the US Attorney’s office for misfeasance or malfeasance in office, abuse of power, and violation of a suspect’s civil rights.
In my opinion, this implies that Special Counsel Mueller handed off the Cohen matter because it is a political/legal hot potato, and any prosecutor handling it is going to get his fingers burned.
Who knows if that's true ... but it seems like a reasonable explanation.