It actually dates back to the 1980's when Shirow Masamune created Appleseed. He wrote in the backstory that the United States of America had been involved in various external wars and even a civil war. It all left the country tattered and torn up. The only way for the country to survive was to divide into three countries.
The United States Of America would still exist, but only inhabiting the states of Wisconsin, Minnesota, North & South Dakota, Wyoming, Montana, Idaho, New Mexico, Arizona, and Colorado
The Russo-American Alliance (or Ameri-Soviet Union in post 1991 materials and the dub) consisted of Alaska, Hawaii, Oregon, California, Nevada, Arizona, Illinois, Indiana, Pennsylvania, Michigan, Ohio, and the entire New England area.
Imperial Americana (The American Empire) would make up everything else, which is pretty much the entire southern and south-eastern portion of the country, including control of Washington D.C.
It is this bit of background info that followed into Ghost in the Shell. GITS, Appleseed, and Real Drive all take place in the same universe, but at different time periods to link them together.
It is the American Empire who are portrayed as the bad guys in the 2nd season. Following an extreme right wing government the likes that both the Reagan, and more recently, the Bush administrations became infamous for with thier foreign policies. If anything, this was a jab at the Reagan era since his foreign policy could be subjectively said to be worse than what Dubbya had.
HOWEVER, it was not an intentional jab at the United States when he wrote the Appleseed series, nor was it a jab at us during the making of 2nd Gig... (at least, nobody ever admitted it was.)
In terms of the anime, The dub only makes mention of Imperial Americana and the Ameri-Soviet Union. No mention of the United States of America. This may just be an oversight, it may be intentionally not included, they may not have known about this, or it just never crossed anyone's mind because it's best not to think too much into things like this when dubbing an anime.
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"A SMARTER hitman would have shot first..." - Major Motoko Kusanagi
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