Well, I'll preface this with I don't own the P99c or P2000sk however I do own the P99 QA .40 and the P2000 v2 .40 with LEM trigger system.
Overall Quality:
-P99 QA: Well made, stable, 10 round mags suck! I'm on the 5 replacement from Walther.
-P2000: Seems slightly more well made than the P99, included two 12 rounders, new factory 10 rounders are only $7
Trigger:
-P99: Love the QA trigger, it could have a better reset for quicker follow up shots but its still quite easy to get good follow ups. Smooth and consistent all the way through
-P2000: LEM trigger is a little light for me but the reset is really short making insanely accurate and quick follow up shots. It takes getting used to but its nice.
Safety:
-Essentially all the same internal stuff between both weapons
Ergonomics:
-Both have interchangable backstraps.
-P99: Very comfortable and solid feeling, no complaints
-P2000: While no complaints about the P99, the P2000 is fully ambidexterous. Slide release on both sides and mag release on both sides. The mag release on the P99 is a little better than the P2000
Accuracy:
-P99: Shot 3000+ rounds through it, I'm accurate, its very good
-P2000: I've shot 300 rounds through it and I'm already more accurate with the P2000 than the P99. And, on top of that, the P2000 has more muzzle flip (because the barrel is .5 inches shorter most likely).
Accessories:
-P99: Make sure you get the new rail system. Holsters are realitively easy to find but considering how long its been out, you would think they should be more easy to find than they are.
-P2000: Standard rail on all varients/years. Holsters are fairly easy to find and the manufacturers that I've spoken to that don't already have something out, are currently working on something. Give it another year and you'll be able to get all of your favorites. I'm waiting on one from Blackhawk or C-Tac allowing me to carry my M3X preattached.
Price: P99 is ~$600 w/ night sights, P2000 is ~$800 w/ night sights. Don't pay more for an SK than you would for a standard P2000, you can find them for the same price if you look. Gunbroker prices are gradually starting to come down on them. But for the record, I got my P2000 w/out night sights but with a Streamlight M3X for $800 brand new which makes the gun itself about $600.
Customer Service:
-Walther/SW: Nice to deal with but I shouldn't have to constantly send my magazines into them for replacements, they are asking for a lawsuit but not recalling all 10 round .40 magazines b/c eventually someone is going to need to use it and its going to fail. They've always been knowledgable, friendly and easy to deal with. Prepaid shipping labels always.
-HK: Personally I think a lot of the HK customer service opinions are not first hand opinions. I haven't had to send anything in to them yet but I've called two or three times with questions and was immediately transferred to an engineer who was able to give me very specific details and answer my question both times. I can't comment on sending stuff in b/c I haven't had to experience that and don't intend to ever need it.
Overall: I think your decision should be more budget related. If you have the money, go for the HK, you won't be disappointed. If you don't want to spend the extra cash, go with the Walther, you won't be disappointed. Definitely handle both before you buy though, I can't shoot subcompact models which is why I opt for the full size ones. I never have problems concealing and I'm only 5'10''/180.
Either way I think you'll be happy and either way, I'm sure you'll buy the other one a couple months down the road! Ha!