Another huge difference is (economically) structural.
The Japanese banking system has been protected from the consequences of bad loans to such a degree that almost no bank goes out of business, no matter how badly it does - or how much of its "assets" are actually uncollectably bad loans. This has led to an gaggle of "zombie banks" that ought to be dead but keep on existing - and in the process keep on dragging money from the government that could be better used elsewhere.
That so far endless problem has been a major drain on growth and the economy in general.
Second problem - the Japanese government has such a MASSIVE tradition of pork barrel public work projects that it makes the US Congress look like rank amateurs. Another drag on the economy, that takes tax dollars from everyone and mostly benefits the insiders who get the contracts.