BaseballProspectus.com: December 18, 2000 - From The Mailbag
Chris Kahrl comparing Willie Hernandez's 1984 to Billy Wagner's 1999
Other factors worth remembering: the DH, and the difference between pitching in Tiger Stadium (one of the easiest places to hit a home run back then) and the final year of the Astrodome.
This comment reminded me of a bias that exists against NL relievers. When you compute things like ERA+ for NL pitchers you use the league ERA as the numerator. This ERA is typically lower than the AL's ERA due to the designated hitter. However, you can probably count on one hand the number of times Wagner faced the opposing pitcher in 1999. Therefore, he is underrated relative to the starters.
I would also wager that NL relievers face more hitters with the platoon advantage than AL closers do, because it seems to me that the NL pinch hits in late-inning situations more than the AL does, but this is nothing that I've studied in any useful way, so I'd likely be better off not even saying it, but there it is, though you could argue that tossing it out there might engage someone in a new area of research, but then again I shouldn't be so brazen as to offer an opinion without any supporting work, but on the other hand, I'm a busy guy with lots to do, so I really shouldn't beat myself up so much for such a small thing as merely tossing out an idea, a trifle in reality, that no one really cares about other than the most hardcore of hardcore baseball fanatics.