I don't know if I would put them in the category as being similar concepts aside from size and having paddle style magazine releases.
The Walther is a double/single action striker fired pistol and is intended to be carried decocked in double action as far as I am aware. I am also not too sure of how fond I am of the decocker being on top of the slide either, have only handled p99 clones in stores, but to me it seems like it would be easier to accidentally activate than one on the frame.
The VP9 has a traditional striker fired pull and it meant to be carried "cocked" all of the time. I greatly prefer having a trigger that is consistent so that do not have to devote more training time to mastering the transition from DA to SA. I cannot speak for the trigger feel on the p99, but the VP9 is pretty good.
I guess what it really comes down to is do you want da/sa or not? I suppose you could carry a p99 is SA, but if you were going to do that, why even buy a gun that is da/sa in the first place?
Of the two, I would greatly prefer the VP9sk. If the Walther ergos work better for you, the PPQ is offered in a sub compact model as well.