I would just like to add that this is one of the main reasons I'm looking forward to HBD. In the SIM, all of the hitting and pitching is based on specific stats from a season in the past. Here, the stats are projected based on ratings, which when you think about it, is similar to RL.
All players have specific attributes - speed, power, contact, arm strength, pitches, glove, stamina - that determine the outcome of each individual AB and games as a whole. Anomalies are visible in RL too and you just have to overcome them.
Let's say Pujols goes into June hitting .200 with 5 HR. Is he any less Albert Pujols than he was last year? No. But for whatever reason - fatigue, not seeing the ball well, pitchers working him really well - he's not producing. So let's say LaRussa moves him down to sixth in the order and puts another hot hitter up top. Is that hot hitter better than Albert? No, but he's performing better RIGHT NOW. And is Pujols any less Pujols batting 6th than 3rd? No, but maybe the shake up gets results.
If after a few weeks to a month, the guy at the top has severely dropped back down to Earth and Pujols is now up around .275 with 10 HR, then Tony switches them back.
Players under and over perform all the time in MLB and though people may question it based on the player's past stats or physical make-up, they certainly ride it. They don't say, "nah, let's keep him where he is...he'll cool off." So why should this be any different? I know it's a computer simulation, but again, RL baseball is based on individual player's attributes or "ratings" and the results don't always line up, so you try different things.