Moreover, unlike Afghanistan, the Germans and Japanese (especially the Japanese) displayed an actual ability to attack American interests not just isolated incidents.
The truth is that with 9/11, there was no government entity to be defeated. The best we could have hoped for was to beef up our own security, and then ignore the countries in question. Maybe go after Bin Laden like we did -- stealthily and in the night.
As much as I would love to rag on Bush, Obama, and Trump, you have to realize that FDR, Truman, and Eisenhower had an extremely homogeneous, nationalistic, patriotic people to lead, whereas bush, obama, and trump all were handed an extremely divided country where nationalism and patriotism were bad words, with perhaps the exception of Bush who got post-9/11 unity for a bit.
FDR was damn near a dictator, a popular one but a near dictator nonetheless. With one executive order, FDR made gold illegal while the USA was still on the gold standard. FDR almost succeeded in stacking the Supreme Courts (and even then, his 12+ years of tenure allowed him to make the courts almost entirely his choice). FDR grew so powerful that we literally got an Amendment to the Constitution to make sure 4-terms as President can never happen again.
Today, there's so many libertarians who just go up in arms about the idea of making Cryptocoins illegal.
Even the US policy towards Japan was rather shrewd.
It's unlikely to see Afghanistan become anymore than what it is regardless of foreign intervention. They don't have the same recent history. It's similar to a Somalia than a Vietnam.
The difference lies in the type of Leaders the US has propped up across the board.