I'm a Walther fan (Own a P99C QA and a PPS, and have owned a P99 QA) and have never owned an XD, so I'm bias that way, but I'd have to say pragmatically that if you have the opportunity to, take both to a range first (or find someone nearby to go shoot with who has one who'll let you squeeze off a couple rounds) and try them.
Based on the 'feel' of the two guns and my relative experiences with P99's (a subjective thing admittedly) I'd go with a Walther P99 any day.
One plus for XD's though is, I bet they're easier to get accessories, holsters etc for. Try finding a mag extension for a P99 or P99C for example (only place I've seen them available involved paying VAT and international shipping, for a $20 part... no thanks passed on that). In fact I have an XD9 IWB holster for my P99C :-/ . XDs are also cheaper, and I've heard nor read absolutely nothing bad about them.