Well, when I purchase a lego from The lego store or LS@H, I track my purchase price as the amount I pay. All the points I accumulate are free money which I use to discount what I pay on sets in the future. This is better than treating the VIP points as a continual discount on every purchase, which I could use it for, simply by applying some points to every future purchase that equal the points gained by the purchase. But some sets don't need the discount to accumulate in value. Since the vast majority of my sets are SW sets, I don't have to buy any set on discount for it to increase in value. They just might take time before they go up.
Now, I would say, any set I'm planning to build and display, I strongly consider and often use VIP points and discount coupons on. That helps to balance out the depreciation, so I don't lose money. I'm very happy with my system for collecting. My goal is somewhat different from someone who might be trying to make money. I'm just trying to not loose money while collecting by trying to keep what I pay relatively close to the products value, which will increase for almost all of them in time.