I think you guys are over thinking. I don't believe the game engine is that evolved.

In my opinion, handling is a GK ability. Even if you translate it more loosely, to ball control, still makes no sense that such a skill would be included in the defensive skills. An offensive player normally has better ball control than a defensive player.

Why do you have to train useless stats? It's the easiest way to balance the game and avoid having to code heavier algorithms to deal with normalization and potential exploits. Just like the illegal formations, that keep you from exploiting some unreasonably unbalanced formation. In the same area, you can't choose what skill you'll train. Just between Defense/Offense/Physical, keeping the skills within these groups balanced. And, once again, they balance these groups not allowing them to differ more than 20 points.

This is my opinion... It's coded like this, because it's easier to code.