My personal opinion is that a smaller weapon doesn't have as big of a screen presence as the P99.
The PPK was smaller than the PPS, but the PPK was already a well known handgun before the Bond movies through the many books Fleming wrote and it's involvement in WWII and postwar sales.
I think Walther would be better off maintaining the P99 in the movies. The general public is starting to identify Bond with the P99. I'm not sure Walther would want to tamper with the success of the P99 in the Bond movies.
Incidentally, I had my first P99 before Bond had his with no idea that Eon had chosen the new Walther for the movie.