Was this a reaction to the fact that consumers weren't really aware of the game without the familiar branding, as made clear by a Google Trends chart tweeted by Destructoid's Nick Chester? (Or recent analyst comments saying as much.) When asked about the apparent change of heart (and art), Activision replied, "Infinity Ward, the original creators of the Call of Duty franchise, has said from the beginning Modern Warfare 2 resides in the Call of Duty universe. This is reflected in the title's package."
The company also said that, "Modern Warfare 2 is the direct sequel to Call of Duty 4: Modern Warfare. We have focused our attention on Modern Warfare in order to most effectively communicate the fact that this is the first true sequel in the Call of Duty series." We agree: letting people know it's a Call of Duty game is probably a good thing.