Well, tennis is also about rythm. If his slice works against every player except Nadal and he uses his slice to get to finals against Nadal on clay, then when he gets to play Nadal his topspin backhand has no rythm, he is dependent on his slice but still cant play the slice, so he is forced to play a topspin backhand on all these awkward positions where he usually just plays a sliced backhand, he is forced to play a tennis very different from his natural game.
I see what you're saying, but players would constantly target his backhand if they knew they'd get the weak topsin response each time, just like Nadal does. He uses his slice to mix the pace and move his opponent around and eventually make room for the big forehand.
You have to remember Federer is using the one hander as well, it's not comfortable to hit over the top of balls hit with pace and depth to that side, and he'd shank a lot more balls than he already does if he followed your advice, quite frankly.