Valve tried doing something like this with Counter-Strike: Source. The more a gun was used, the more it cost, and vice versa.
And it failed pretty badly. The deagle, a gun that usually costs $800, cost upwards of $23,000. According to tvtropes, a gun costs negative money at one point.
The point, is, popularity is not necessarily correlated with balance. If everyone started using harpoon squids, the game will interpret harpoons as being supremely OP and nerf them out of existence while giving every other gun a boost.
Almost every Goldfish I see has a Hwacha on its front now. Does this mean that the Hwacha is overpowered? No. Nerfing the hwacha at this point will just make less people use the goldfish in general, which is counter to what the system is trying to fix.
I do agree that meta builds are seen a little too much. But there are better ways of balancing a game than leaving it in the hands of a math equation.