They are different. Do you want a single action / double action with a hammer in the FNX-9 or a double action only in the M&P? There are pros and cons to both.
I prefer a SA/DA and the FNX-45, I decided it was a good replacement to the 1911 after my wife bought an FNX-9 for herself. Her reasoning had nothing to do with SA/DA or anything like that, she liked the grip and the sights, but after putting it through its paces, I decided that the FNX-9 was a pretty good choice.