S&W has two polymer pistol lines. Think of it as a budget line and a premium line. S&W owns the rights to both.
The SW99/990L line was a licensed collaboration between S&W and Walther. S&W only made the slides and barrels for the SW99/990L models and had to buy everything else from Walther (magazines are Mec-Gar). You can imagine how that might lessen the potential for a return on their investment.
S&W also has total control over the development of the M&P.
The 99 series is a fine pistol line and I also feel the SW99 models were excellent values for the money.
I also own a SW99 compact (9mm) and a standard model (.40 S&W). I've helped support over 50 SW99's (one of which was my issued SW99) and the occasional P99.
Having been trained as an armorer for both the SW99/P99 and M&P series I find advantages in both, but I feel the M&P arguably offers some further refinements.
The sear housing block of the 99 series is expensive and somewhat overly complex. Also, the ejector is molded into the sear housing block of the 99 series and isn't exactly as robust as that used in the M&P series. Replacement of the ejector requires replacement of the entire sear housing block in the 99 series.
The extractor design used in the 99 series is not a fitted part and is held in the slide by a spring loaded plunger. That's convenient and makes for easy removal and replacement. It's also caliber dependent. The M&P extractor is the same across the model line and is much more robust, although it's technically a fitted part (meaning it may require fitting in some slides). Removal of the M&P extractor is not as simple of a procedure as with the 99 series.
The grip inserts of the 99 series just change the dimensions of the back strap and lack the ability to change the palm swell dimensions. Also, the frame incorporates more of a grip tang to protect the web of the hand in the M&P.
The slide stop lever spring on the SW99/990L series has a hooked end which is somewhat exposed inside the magazine well of the grip and which can be caught and bent if an owner is inattentive during cleaning. I know of at least one large agency which apparently couldn't get its people to stop snagging and bending the springs, so they finally sent them the shorter spring used in the P99 models which has is looped and closed at the rear (and also a bit weaker in tension).
The M&P series uses a stainless steel guide rod assembly.
Although Walther has revised the 99 frame and apparently increased the thickness at least at one point (which I only noticed because of a change in sear housing block dimensions), the M&P also has a steel sub-chassis reinforcing their frame, which also holds the coil pins securing the sear housing assembly and the locking block.
The 99 series frame rails are incorporated in frame insert fixtures molded into the frame ... except for the compact model which has the rails incorporated in the locking block. If a rear frame rail in a compact model or any frame rails in the full-size models were to break off the whole frame would have to be replaced.
The M&P series frame rails are incorporated in the sear housing block and locking block, and in the event of a broken frame rail the rails could be replaced by an armorer by just replacing the sear housing block or the locking block (without having to replace the frame). On further note, the frame rails used in the M&P series are referred to as rocker rails, and their design allows for self-centering as any wear may occur over the service life of the pistol, and which we were told is an aid in accuracy.
The rear sight bases are much more stable in the slide's dovetail and don't require the spring loaded plunger to hold them in the dovetail. The front sight post is also mounted in a dovetail and can be drifted by an armorer, if necessary, to aid in adjustment.
The slide serrations are less slippery with wet or sweaty hands on the M&P slide.
The take down catch on the 99 series is larger than the slide lock lever used on the Glock, but I never really cared for how it felt, myself. The spring loaded take down catch pin has to be carefully seated at both ends. I do like the barrel lock used on the 99 series, and I think the lock spring being a coil spring is also an improvement over the flat leaf spring used in the Glock ... although the 99's coil spring can be seated improperly in the frame's stepped hole and can become damaged. I think the M&P take down lever design is a bit simpler and more robust than either the 99 series or the Glock, although the lever does have to be aligned properly during field stripping disassembly/reassembly (and attention has to be paid to the small taken down lever retaining wire by an armorer during reassembly so it remains where intended).
The visual loaded chamber port on the M&P is arguably easier to see and use than the dab of red paint under the tail of the 99 extractor.
You aren't the first person to state a dislike for the paddle magazine release catch. I happen to like it, myself, though (before Walther extended it in their later production model line, at any rate).
There are some other minor things here and there which overall make the M&P series arguably a bit of an improvement over the earlier SW99/990L series, as well. If not 'improvements', then perhaps just refinements in another direction. Just depends on your perspective.
I think S&W has a winner on their hands with the M&P series. That doesn't mean they aren't still continuing to refine it, though.
Don't mistake my comments and thoughts as meaning I dislike the SW99, because I don't.
Matter of fact, I like my SW99 compact 9mm pistol quite a lot. Although I did have to replace a couple of the Walther parts early on to correct a problem, once that was done it's been a reliable, trouble-free pistol and I'm approaching the point where I'll soon have fired 10,000 rounds through it. I've replaced the striker, recoil & extractor springs for preventive maintenance.
Like most 99 series pistols with which I've had experience it took a while for the trigger to feel lighter and smoother than when NIB.
The practical accuracy of the SW99/P99 pistols I've used have been very good. Excellent, even. My SW99c is no exception. I can actually experience better consistent practical accuracy with my SW99c than with my 3913 or G26. If I didn't already own the SW99c I'd probably buy a M&P 9c ... but since I already own the SW99c (as well as a 3913, CS9 & G26) I don't really feel the need for a M&P 9c.
Just my thoughts.