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Brian H (misunderestimated)It’s a baby boomer generated list that overrates the big names from the 1940's through free agency (the guys that the voters saw play during their formative years). It also ignores the 19th century stars and gives some (but not nearly enough) credit to the Negro League greats. These two groups are admittedly the hardest to rate but I think even a conservative approach would give them more credit. That said I'm surprised Mickey Mantle scored so poorly. http://www.baseball-reference.com/m/mantlmi01.shtml) He is usually at the top of such lists and (at least in this case) I think they may have underrated him! He was certainly, better than Joe DiMaggio (http://www.baseball-reference.com/d/dimagjo01.shtml) unless you are willing to give a lot of speculative credit for what DiMaggio might have done during the war.
Apart from those general errors, the biggest mistake is Wagner. I would put him easily in the top 5 all time (probably at 2 or 3) . If they had an MVP award akin to ours during his career he would have won more than Bonds (the same with gold gloves) At least until very recently the Shortstop were inferior hitters. Wagner however was among the best hitters in all of baseball for most of his long career. If you look at the leaders Wagner was among the leaders at in virtually every offensive category during his career. (http://www.baseball-reference.com/w/wagneho01.shtml) In short he was most complete position player in the games’ history, he played a crucial position, he was a winner, and he was a great teammate. He tied Babe Ruth for second just behind Ty Cobb (http://www.baseball-reference.com/awards/hof.shtml) in the inaugural Hall of Fame voting (which was a bit screwed up) in 1936.
With the Negro Leaguers, the consensus among the people who have really given the issue the most thought is that Oscar Charleston (http://en.wikipedia.org/wiki/Oscar_Charleston) was the greatest all around player and should rank ahead of the more famous Josh Gibson, Cool Papa Bell, Buck Leonard and Satchell Paige. Predictably those guys are from the next generation.
Significantly overrated: Koufax, Joe Jackson, Clemente, Lou Brock, Sisler, Bill Terry, Nolan Ryan and Joe DiMaggio.
Underrated (as of 1998): Collins, Lajoie, Lefty Grove (should be in or around the top 10) (http://www.baseball-reference.com/g/grovele01.shtml) Joe Morgan and Tris Speaker.
Should be on the list:
1. More Negro Leaguers (egs. Joe Rogan, Joe Williams, Pop Lloyd)
2. I believe the earliest on the list are Young, Wagner and Lajoie all of whom played in the 1890’s. Of those only Young 9 http://www.baseball-reference.com/y/youngcy01.shtml) played the better part of his career before 1900.
Of the earlier players missing at least some of the following belong: Delahanty, Anson, Kid Nichols, Brouthers, Billy Hamilton, Buck Ewing, Connor and probably at least one more Pitcher like Clarkson, Rusie or Radborne)
4.Three Finger Brown;
5.Floyd "Arky" Vaughan (there aren't enough shortstops on this list at all and he's among the top few all-time)
As to what to do as of now with Bonds, Clemens and anything else from the past several years:
With Bonds and anyone else suspected of using PEDs to increase their power and/or durability I think they should be credited rather conservatively since we really don't know how rampant PEDs were, how much certain individuals benefited over and above the other players they had to compete with. All things considered I think Barry easily has to go in the top 4 or 5 but I can't see going much further until we have a better perspective.
I also would bump up Maddox, Clemens and Rickey Henderson. I'm holding off on putting Clemens (at the moment the one I rank highest) ahead of Johnson, Grove and Young until the dust settles.
Based on the numbers alone the following players probably merit strong consideration (depending, of course, on whether you want to preemptively punish some of them for using PEG etc.): AROD, Sosa, Jeter, The Big Unit, Pedro, Palmeiro, IROD, Piazza, Frank Thomas, Glavine, Manny Ramirez etc.