My only exposure to the SW99 45 was for some extended T&E.
Personally, while I happen to like the 99 series, I just didn't care for the SW99 chambered in .45 ACP. It was reasonably accurate enough. No feeding/functioning problems were experienced or observed during the T&E period by any of the shooters.
It just wasn't as 'easy' to shoot as some of the other .45's being used according to some shooters. (The M&P series had not yet been released.) I found the SW99 45 accurate enough from a practical perspective, but not as 'easily accurate' as the HK USP 45, for example. I wasn't the only shooter to make this observation, either.
On the other hand, I've found my M&P 45 (full-size) to be amazingly accurate, even when the trigger was on the rather heavy end of expected tolerance when NIB. The consistency of accuracy of my M&P 45 has easily rivaled that of my 1911's (both Colt & S&W models). It's easily become my favorite .45 to choose for range training.
Now, if you can find a NIB SW99 45 with the lifetime warranty available it might be helpful. The reason I say this is that the Walther parts can be pretty expensive if you have to pay for them. The sear housing block, for example, costs approx $100 (retail) if it has to be replaced ... and since the ejector is molded into the housing block, if the ejector ever breaks the housing block must be replaced. Better to have this done under the S&W lifetime warranty, if at all possible.
Personally (and this is entirely subjective), I find the grip dimensions and overall ergonomics of the M&P to be superior to those of the SW99 45. The grip girth and height seem larger in the SW99 model than really needed for the 10-rd mag capacity, and the 99's backstrap inserts don't offer the sane extent of interchangeability as the M&P's grip inserts (which also change the palm swell).
There are some refinements and advantages found in the 99 design, but I feel there are some further refinements and advantages found within the M&P series.
If possible, being able to try an example of each would probably make selection an easier process for someone, but the availability of a used, or rental, SW99 might make that difficult or problematic.
I happen to like the 99 series best when chambered in 9mm (much like I prefer the Glock series when chambered in 9mm).
I happen to like the M&P best when chambered in .45 ACP.
Or, to put it this way ... which is very subjective, and is only my personal opinion ... as much a I liked the SW99 series (carrying an issued SW99 40 and owning both 9mm & .40 models), I was ready to order the SW99 45 when it was announced.
Once I handled and fired the T&E SW99 45, though, I changed my mind (from the very first range exposure).
I'm much happier with the M&P 45.
That's just me, though.
There are some pleased owners of the SW99 45.
Try one of each at a range if at all possible.