With baseball, it's so tricky because for field players, defense tends to get severely overlooked (and is very difficult to measure objectively). Plus, pitchers are essentially a separate category.

I'm not well-versed in boxing, but have you thought about looking at the G.O.A.T. for MMA? It's a relatively new sport, I know, but I think there are a lot of candidates that have their own unique accomplishments and flaws--off the top, guys like GSP, Anderson Silva, Randy Couture, Fedor Emilianenko, Royce Gracie all have cases, as well as counters to said cases. It's a fascinating case study, methinks.

Also, while I don't know much about the following sports, has there been any consideration to discuss the G.O.A.T. for track, gymnastics and skating?