Come on, it looks more real with AF turned on, you gotta agree there. Now if Konami fucked up and didn't set it up correctly, this is another issue. Players shouldn't tire so fast. But then again, you shouldn't play every player full 90m every week (every game), that's unreal too. You can try to rest top players at least an entire half every 2-3 matches, and consider resting them a full match with weaker teams. As long as I played, I realized that (in MLO) resting a player 1 full match, once his AF bar is half full, is almost enough for him to be like new for your next game.
Someone has said on this forum that it's too bad that Konami can't keep track of how the game actually goes, in order to properly display the Accumulated Fatigue. I.E. if i'm winning 2, 3-0, i barely use Turbo. Just simple passes, a nice possession game. This never tires players so much. However in PES, there is almost no difference whether you play a nice, calm game or you go all out attack at full speed really. That's bad.