There have been a few posts recently where the difference in quality between the leagues has been a contentious topic in the comments section. However, nobody is arguing with the fact that the AL is unquestionably the superior of the two. Here a few quick pieces of data that back up that supposition.
AL Interleague Record 2008: 149-103, .591 winning percentage
AL Interleague Record 2009: 137-114, .546 winning percentage
Add that to the fact that the AL hasn't lost an All-Star game since forever ago, and it looks like the AL has been kicking around the NL for over a decade. However, the AL hasn't been quite as dominant as those facts suggest. In the eight years preceding 2005, the NL actually had a winning record of 988-960 (.507) against the AL. That said, the last five years have been really bad for the senior circuit. The question is why.
Many people immediately point the finger at the DH, but it doesn't seem like that could be the answer, or even a big part of it. If that was the case, it wouldn't make sense that the NL found sustained success against the American League when they started playing each other for the first time. In fact, I think that in interleague play having a DH is arguably a disadvantage. I don't have any data to support this, but it seems like it would be easier for a major league hitter to adjust to not playing defense than for a pitcher to adjust to hitting major league pitching. Anyway, the DH rule doesn't seem to have much bearing on the difference in quality of play between the two leagues.
The second major factor I could think of was payroll.
2009 Average Payroll for the AL was slightly over $93 million compared to around $84 million for the NL. This difference of around 10% is fairly consistent with the numbers for 2008. However when you look at the median payroll for each league in 2009, the AL sports a figure of about $81 million to the NL's $79 million. This is starting to get at what I think the problem is. The Yankees skew the AL on the high side. You could argue that the Mets do the same thing in the NL, but they still spend $50 million less and their exorbitance is spread over 2 more teams than they Yankees'. What really skews it for the NL is its bottom four teams.
There are four NL teams with payrolls lower than the most miserly AL club. About three of these teams spend on the order of half of the lowest playing AL team. I think this is the biggest source of the disparity between the two leagues. It has been shown (I don't remember where) that having a couple of players on your team that are well below replacement level can far outweigh the production of a couple of superstars.
Take the Royals and Pirates for example. Both of these teams are terrible, but they are arguably terrible for very different reasons. The Royals were a victim of ownership for some time, but for several years have proven that the real problem is the way the front office spends the money that they have finally been given. This is why many of us Royals fans are not always optimistic about the future of the club even if the farm system provides us with some good talent. The Pirates are largely terrible right now because their ownership has not really ever invested in them at all. A payroll around $30 million is inexcusable when they get help from revenue sharing to the tune of nearly $90 million (according to Soren Petro and Jayson Stark).
Payroll doesn't directly translate into wins (Mets) but a higher payroll does give you a better chance to win. For the majority of the AL, teams are awful because of management, not because of ownership. In the NL, this isn't always the case. Some teams are unlucky enough to have both be awful.
If the NL and the AL are to be equals again anytime soon, there are several National League owners that need to quit taking money from revenue sharing and putting it in their pockets and start investing some actual money in their ballclubs.