Hard call. Not sure I'd have a consistent answer for myself, let alone something to offer anyone else.
I own a 3913 and have done some shooting with a M&P 9c. I also own a M&P 40c & 4040PD.
Between the 4040PD and the M&P 40c ... the M&P is the better handling, more controllable gun under live-fire.
Now, the 3913 is one of my all-time personal favorites when it comes to a compact, reliable, fast-handling and accurate 9mm pistol. I think I've owned mine since '98. I really like the balance.
However, my SW999c (compact 99 series 9mm in the standard configuration, what is now called Anti-Stress by Walther) has a much better trigger in both DA & SA than my 3913. On any given day I can often wring a bit more practical accuracy out of the SW999c, too. The grip profile feels smaller, as well. Then, there's the 10-rd vs. 8-rd magazines to consider, I suppose.
Anyway, the M&P 9c I handled and tried on our range, while not having quite as smooth and nice of a trigger as my other 9's (it was the first time the M&P 9c was being fired, so the trigger hadn't had a chance to break in) ... did offer a very nice balance & heft. It was also quite accurate (despite the trigger) and had outstanding recoil management and controllability. It made me reflect that I probably ought to have bought a M&P 9c instead of the M&P 40c.
Now, I have no plans to ever get rid of my 3913 (or CS9), nor my SW999c. My pair of Glock G26's serve me well for their intended purpose, as well.
That M&P 9c certainly made a good argument for owning one, though.
One of the other instructors just bought his 3rd M&P, a M&P 9c. I know he has come to like some of the Apex parts in a couple of his M&P's. The first time he test-fired his new M&P 9c, though, in box-stock condition, he was very enthusiastic about how well it handled and fired, and how much better the stock trigger was compared to his other M&P's.
Now, aside from being a long time 1911 owner & user, I happen to like a good traditional double action (DA/SA) pistol for most defensive needs. I spent 20 years with various issued 3rd gen S&W's (and I don't mind my early production Ruger KP90DC, either

).
The M&P model line has shown me that S&W can indeed adjust to the current market demands for a lightweight, plastic service weapon and offer some interesting refinements to the concept.
Bottom line, though, is that I tend to prefer the M&P chambered in .45 ACP best.
If I were still working as a regularly employed cop, I'd prefer to carry an issued M&P 45 or 45c instead of the 4566TSW & 4513TSW models I carried prior to my retirement. Go figure.
Then again, if I'd had the opportunity, I'd have willingly carried an issued 3913TSW instead of the 4513TSW I was carrying in my plainclothes assignment, too.
See? Told you I didn't have a clear answer for myself, let alone anyone else.