My vote would've gone to Derrek Lee - he was ever-so-slightly the better offensive and defensive player - but Pujols has become one of the best, most consistent hitters the game has ever seen, so it's not like he was a bad choice or anything. Besides, St. Louis made the playoffs while Chicago fell short, so it's not like this was impossible to see coming.
Three cheers to the BBWAA for selecting a qualified candidate instead of Andruw Jones. Three jeers to the BBWAA for placing Jones ahead of every non-Pujols player in the NL. Andruw Jones was nowhere close to being the most valuable player in the league; he was 17th in the NL in VORP, and it's not like his defense did him any favors (according to the best metrics we have available).
Better still, where VORP had Roger Clemens #4 in the league, he finished #22 in the voting, behind such luminaries as David Eckstein, Pat Burrell, and Jimmy Rollins.
And hey, just for good measure, the .686 OPS'ing Jose Reyes finished tied with the totally awesome Brad Lidge, with a single 10th place vote apiece.
I guess it really doesn't matter, since the voters wound up choosing Pujols anyway, but looking at the rest of the standings just goes to show how much irrational thought still goes into the whole process.