I used to be one of those people (arguing with those pointing out the flaws). I remember making many a dumb post in this regard.
Part of baseball is hope but looking at the cold reality of a players probability to be effective tends to burst the hope bubble. And that irritated me. I just wanted to enjoy my game without all this doom and gloom.
Then I figured out that all we are talking about here is probability. You can assemble the worlds greatest team, with the best stats possible on paper, and you can still end up with the Epic Fail (my new favorite phase). As is often said, you still have to play the game. Even if you have a 95% chance of wining there's still that 5% chance you don't.
Better stats = more probablity that your team will win. Worse stats = more probability that your team will lose. Don't we all want a better chance at winning?
Ultimately the argument has little to do with individual stats and numbers. The argument is about what players give you the best probability to win. The stats only serve to determine the probability.
Once I got my head wrapped around that baseball became a lot more enjoyable.