I do tend to prefer the M&P series to the Walther 99 series (including the SW99/990L), but I own a couple of SW99's and carried an issued one for a few years.
There were some revisions and improvements made in the SW99 line along the way. Once S&W helped figure out that the .40 S&W mags needed revision (and provided the info to Walther, who passed it on to the mag company) it helped resolve some feeding issues which had been reported with the .40's made in both manufacturer's model lines.
I was told of some other changes here & there, too ... such as the locking blocks being dressed better, the extractors being better polished, etc.
The use of the open-ended/hooked slide stop lever spring S&W requested for their licensed model line was a stronger spring, but it came with a potential disadvantage. The hooked end could be snagged when the frame was being cleaned if someone was inattentive, and the spring bent. Replacing the spring meant removing the locking block, which meant removing a rolled steel pin. I met a few armorers who preferred not to remove that pin themselves.
S&W used the mag catch lever spring as their standard extractor spring, which was heavier than the original extractor spring and was reported to offer better functioning in the .40 & .45 models. At one point S&W advised armorers to reverse the orientation of the extractor springs in the slides, too.
Then, there was reportedly the use of different dimensioned trigger bar guides in some SW99's which caused some light strike issues due to the trigger bar being cammed down and releasing the striker a bit too soon in DA mode. One of my SW99's had that issue and I was told how to resolve it by a repair tech working in the Walther America facility. He had encountered a few P99's with the same problem (which makes sense since it was the same Walther made parts in Walther frames involved). I learned later on that Walther had a range of differently dimensioned trigger bar guides which were used, but that Walther hadn't informed S&W engineers of the tolerances or provided a gauge until late in the SW99/990L's production. The AS & QA models use different trigger bar guides (and different striker springs, BTW), in addition to the obvious difference of the sear housing block not needing to function in single action mode.
I've seen some differences in production involving SW99 .40 barrels made at different times. The differences included how the muzzle crowns were cut, the barrel tabs were cut & finished, the feed ramp shape & finish and the shape of the chamber mouth.
A change which S&W made to enhance functioning during unlocking/locking involved making a machined relief under the barrel at the rear, where the bottom of the barrel needed to clear the top of the recoil spring assembly. (Ever hear the scrunching/screeching noise in an early SW99 or a Glock when the slide was being manipulated by hand?) I saw a couple of different length relief cuts on SW99 .40 barrels once this change was introduced. Nice refinement.
At one point Walther changed the internal frame dimensions in the area of the sear housing block, too. I only figured this out when I was replacing a sear housing block in an early production SW99 (broken ejector, which is molded into the housing block) and found the dimensions of the block and its bottom pin were different. The enw block wouldn't fit into the older frame unless the pin from the older block was installed in the new block. I confirmed this observation by calling S&W and asking about any recent changes.
My SW99's have provided excellent service ... once I replaced the early .40 mags with the revised ones, and corrected the trigger bar guide tolerance issue in the 9mm model. I've fired many thousands of rounds through them, in addition to issued models.
Of the 50-odd SW99's (and at least 1 P99) I've helped maintain and service, I've only had to replace a handful of broken or damaged parts (Walther parts) over the course of several years. I can think of 2-3 ejectors (sear housing block), a couple of extractor springs and an extractor, a slide end cap, a couple of rear sights & sight base plungers, trigger bar guide. That sort of thing. More parts for normal service (springs) and when revised parts were provided (barrels, extractors & mags). Some of the guns have had as little as a couple or more thousand rounds fired through them during that time, and a few others have edged upward of several thousands of rounds. A couple of them have exceeded more than 50,000 rounds according to one guy who shoots his 3 SW99's quite a bit. He hasn't had the time to reach as high of a round count with his 3rd gun, but he's working on it.
Overall, I always felt the 99 series incorporated some refinements over the Glock series, and I think the M&P line incorporates some refinements over the 99 series. I've been certified as an armorer for all of them and have some experience maintaining, owning and shooting examples of each line. I own a couple of each maker's models and find them all serviceable for their intended roles.
When I buy another plastic framed pistol, though ... which is likely ... I think it's a safe bet that it will be another M&P.