But the truth is that there isn't much difference between making a list of "best value" and "best players." You do expect a 1st overall pick to turn out to be a good player--but not a Hall of Famer. Few 1st overall picks go on to become legends. So the discount for being a 1st overall selection isn't large enough to knock a player like Manning off his perch at #1.
You can look at it this way. Would you rather have Peyton Manning and a 6th round pick or Tom Brady and Ndamukong Suh? The smart pick is Manning, who produced twice as much Win Probability Added (40 vs. 19.8) and twice as many Expected Points Added (1477 vs. 713) as Brady this past decade. Suh would have to outperform Brady for you to want them over Manning.
This probably seems counter-intuitive, but it makes sense if you consider that talent in the NFL probably has some type of Pareto distribution. The expected value for the best player in NFL history, the expectation of the 1st order statistic in a sample of thousands, is going to be massive vis a vis the expected value of the 50th best (an overestimate of what we expect a 1st overall pick to be worth).