It seemed to me the author was making the argument that Billy Beane's tactics, which once were unique, are now widespread and without that advantage, his team stinks.
So... it sounds like he did change baseball. At least he changed the appreciation of OBP and Slugging Percentage. This article's conclusion is confusing.
The Seattle Mariners were an absolutely terrible baseball team in 2008. Their front office had made a lot of bad decisions, so the new regime in 2009 didn't have much in the way of money or other resources to build their team. They focused on getting a lot of defense-first players, and turned in a very respectable season.
Also, Oakland was thought to be a contender this year before injuries hit. That's why Beane traded for Matt Holiday before the season started. Then a ton of injuries hit the A's and they went nowhere. But they were definitely in the mix.
Finally, the Yankees are always going to look good the year they sign the top three free agents in the market for a combined half-billion dollars. Those contracts are going to look pretty awful in five years though, thus leading to the recurring, "How the hell are the Yankees not winning with twice the payroll of everyone else?" in the following years.
Market inefficiencies don't last when a book is written about them. Not that surprising.