I "have" both. Actually, my wife has the XD9...
I'll have to say, as much as I like her XD, I still like the P99 better. Not because of ergonomics, the XD really comes close to the feel of the P99. The trigger on the XD is probably better than the P99 QA. My wife's XD trigger feels about like the single action on my P99 AS (around 5 pounds or so).
I do not believe that the XD will be more reliable than the P99. They are both modern duty firearms and their reliabilities are similar enough to be dropped from consideration.
Safety is a similar point. Though the XD has a grip safety, both guns WILL NOT FIRE unless the trigger is pulled completely and evenly to the rear.
The biggest difference between the two is definitely the finish. The P99, hands down, has a better, more robust finish than the XD. Some XD owners report occurances of rust on their slides. We haven't found any yet on my wife's (we keep it wiped down with oil). So, if you're new to guns, taking care of them and such, you might be better served by the P99 and it's better tennifer finish. I think 100 extra dollars is WELL worth getting a better finish! This is especially true if this will be a nightstand gun. Ya know, one that doesn't get taken out and wiped with oil very often...
If the finish doesn't bother you, get the XD. You will not be disappointed. Actually, the XD is the gun that has impressed me the most since I got the P99. That feeling when I got my P99, the awe and happiness while exploring all of it's great features, was also apparent when we bought my wife the XD. Luckily, you haven't chosen GLOCK. I think you'll agree, handle a glock, then handle an XD, the XD just feels like a better gun. So, again, if you don't mind the finish, get the XD, it is just as good as the P99 and a bit cheaper (based on my experiences).
-stunks
P.S. sorry for all the edits, kept thinking of stuff I wanted to mention