I have a friend with both a Glock 23 and P99 in .40.
The Glock is okay, but in .40 suffers from some ugly muzzle flip. But, it is what it is. Cheap mags, simple and reliable. It's basically a nicer finished AK.
The P99 has a lot of features. Full cap mags are on the expensive side (about 2x of Glock). It is however, nicer to shoot, and appears to be a bit more accurate. The interchangable backstraps are very nice to accomodate everyone from huge hands (me) to little girl hands (my friend). A lot of comments have been made about the trigger on the P99. I also thought it was horrible until we learned the secret. The first DA pull is very long, but not heavy. However, afterwards, if you do not release the trigger all the way, it is super short. I was pulling supre quick double taps consistently.
So, the question is...which do you want? My suggestion would be to play with them first. See which fits (keep in mind the backstraps) and what your budget is.