I think this, at least partially, is the culprit behind being slow. Quality requires time, years of practice, sweat, dedication and experience. And it works really well for craftsmanship. Japan is well known for it's craft, art, cuisine and aesthetics - even in trivial cases like design of manholes or disposable shopping packages. Unfortunately, the same doesn't seem to work for technology, especially for IT. Learn a language/framework today, forget tomorrow, rapidly switch to more efficient solution, keep up with industry standards and everyday learn something new. There's no place for "learn once - master whole life" concept in current enterprise environment. Maybe with exclusion of basic principles. Everything else change on a daily basis. Yet, Japanese web pages tend to look like messy amateur pages on GeoCities 20 years ago and financial institutions wouldn't change for ages (actually, their online pages looks even worse.)
I do disagree about restaurant lines, though. I've yet to see so well organized crowd. And people do know what to order when they reach the counter because in most places they have a menu in their hands long before they get there. And any other lines, on that matter, especially when you compare Western train/metro stations.
Restaurants ( especially soba / ramen ) are so efficient it's insane.
I should have clarified, I'm talking more about coffee shops / cafes ( 喫茶店 ).