Wow, I just read through this whole thread. I think that Shady's last post is quite possibly the most valueable post out there, as it points out exactly why it is nobody's job to run a team but the owner's.
Player values are OPINION and OPINION only. Someone mentioned earlier that someone dropped Joe Horn for Colston last season. Now... what if the commish had stepped in to protect this "foolish" owner from his own "stupidity". Guess who looks like a JACK### now?
It's every owner's right and privilege to run their team as they wish, using whatever system of analysis and decision-making that they want. If I want to prove that running my team via the roll of a die, darts on a target, guidance of the stars, or the position of finger bones in chicken blood, is the best way, it's my right to do so.
If you can't predict the future, the only thing as a commissioner that you can possibly do (or want to do) is to simply confirm that they are trying to improve their team IN THEIR OPINION. Simply ask them, "Hey, this is an interesting move - whatcha got up your sleeve?" If the response supports a belief that they are trying to improve their team, then you need to support them.
Any league with rules (such as this or league vote on trades, etc.) which unnecesarily restrict owners from running their team in the fashion they want, is a league that i would not want to be a part of.
Free will, baby. It's for everyone!