WAR (or Sean Smith's version to be more precise) is the base of WAR + WAA. Proponents and skeptics alike have offered a multitude of reasons why WAR is imperfect. These issues include: debate over what the best replacement level should be, how to deal with the questionable defensive data, limited data on the impact of catchers, how to handle BABIP and HR/FB% luck, what to do with league quality adjustments, etc. I am well aware of all of these concerns and consider them all. One of the biggest questions for some is if WAR (which compares players to a replacement player) is too much of a compiling stat and does not focus enough on peak or dominance. I agree to a point that it does not always paint an accurate picture of dominance or pure "greatness". Therefore, I use WAR + WAA (which only counts how much better a player was than average and eliminates the replacement component) so that peak/dominance is given a little more weight.
Unfortunately, even WAR + WAA is not all-encompassing. From this point on, I look at a list of other factors in no particularorder:
1. League quality
2. Postseason success
3. Park factor issues (assumptions) that may be unfairly helping or hurting a particular player's WAR
4. Peak dominance beyond what WAA captures (how dominating was the player at his very best? Top 3 or 5 seasons?)
5. Defensive issues in Total Zone that could be unfairly helping or hurting a player's WAR. What do the other available defensive metrics have to say about the player?
8. Missed time due to wars, labor issues, segregation, death, etc.
9. Subjective elements - such as historical perception
Notes: I change the results all the time and do not take my own list very seriously. I feel like I have a pretty good ranking overall that I am pleased with. Enjoy!
As of right now, I do not consider PED issues/allegations in my rankings. I have in the past and I may someday again.
WAR + WAA totals DO include any pitching contributions that the regular position player may have had.
I do not list WAR + WAA for catchers, since it really isn't fair to compare their position and lack of available replacement level "points" with the other positions. I do use WAR to compare catchers with each other. As of now, Baseball Prospectus has the best tools to evaluate catcher defense and includes pitch framing. I use BBPro heavily when evaluating catchers.
So why use WAR as my foundation?
A lot of things have to be considered when ranking players. Some of these are: power, on-base ability, longevity vs. peak, postseason success, park effects, baserunning, defense, strength of opponents played, league quality, luck, etc. WAR considers most all of these things and most of them fairly accurately. While ranking, I could go into detail about how each of these factors impacts a player's rankings, but a single number makes it a lot easier and not much less accurate, if at all. Whatever is not covered by WAR can be easily added to the evaluation.