I was talking more about the system itself as opposed to the method of determining worth within the system. What should determine value is certainly a debate worth having. Since you brought it up, is using more modern methods of determining value going to mess with the accuracy of those methods? For instance, if using WHIP, strikeouts and FIP is used to determine arby numbers then it would stand to reason pitchers would pitch to get those numbers. Does that actually lead to a more productive player if the goal was the stat vs the end result?
This is anecdotal evidence but Zack Greinke said as much a few years back. He thought, reasonably IMHO, that pitching to get those stats would lead to better production. His numbers went up but his results as it pertained to actually winning games went down. Changing the goal to get strikeouts instead of a save wouldn't necessarily lead to contributing to more wins.