I think between the two, you are going to have to decide what it is you want in the pistol and how it shoots for you. I know both the P99 fans (and I am one) and the Glock fans (I am not) which will swear up and down theirs is better.
The P99 for me is more accurate and I like the DA/SA availability. The front sight interchange really does not do a whole bunch because out of the box it should hit the dot at 25 m. The grip selection allows the customization of the hand.
The P99 40 has had its detractors and many will post here what a big hunk of $hit it is, but I own one from the second production year on and it is my daily carry.
Accessories are in short supply, and there is only one place to get service (2 if you count S&W). It is not a sell out to buy the P99, the SW99 on the other hand directly supports the CLintonistas.