(technically 26 in the AL due to a tie) players in MVP voting in both leagues, the player with the highest WAR finished 21st and 24th in voting, respectively. Jose Rijo had a WAR of 10.1, slightly higher than Barry Bonds (9.9) who won in the NL and finished 21st. Kevin Appier had a WAR of 9.3, well ahead of AL-winner Frank Thomas' 6.2, and finished 24th. Eight more AL players had a higher WAR than Thomas: (in order of voting finish) John Olerud, Juan Gonzalez, Ken Griffey, Jr., Rafael Palmeiro, Jimmy Key, Kenny Lofton, Chris Hoiles, and Randy Johnson.

Subsequent years were not nearly as egregious. For the next 19 seasons, however, only 4 times did the WAR leader in both leagues finish in the top 3 of the MVP voting. It looks like it wasn't until about 2012 where the WAR leaders were consistently at the top of the MVP voting race in both leagues.

Another bad year for the AL was 1984 when Willie Hernandez won the AL MVP with a 4.8 WAR and Ripken finished tied for 27th with a 10.0 WAR, which was actually an improvement on his 1983 season when he won the award (8.2 WAR). In 1982, Andre Dawson had the 2nd highest WAR and finished 21st, while Steve Rogers had the highest WAR for a pitcher and finished 2nd in Cy Young voting, but didn't receive a point in the MVP voting. Six other pitchers did, with Bruce Sutter (3rd in Cy Young) finishing 5th.

TL;DR version: I need to stay off baseball-reference.com