I think the bigger issue is how the government and local residents are pushing for reforms and thus, the massive crowds are spoiling the experience for others - which is why more restaurants are banning or segregating foreigners, more onsens seem less than thrilled with foreign visitors, we're losing the tax refunds (due to excess and fraud), airport arrivals are a nightmare, etc etc. This isn't unique to Japan, there are many places in Europe where locals are far more in-your-face about trying to get rid of tourists altogether.

Of course if the Yen drops from 150 to 100, this will all 'self-correct', but for now adjusting itineraries and expectations are a solid step towards sanity especially for more frequent or experienced visitors who really should be looking for more off-the-beaten path places to spend time. I would never go back to Senso-ji unless we have an invitation to the off-limits temple area in the back, but I would gladly revisit the bonsai museum, or Showa Park with its beautiful Japanese garden. It's been on my list for years, but the timing needs to be right to visit Hitachi Seaside Park. I also suggest looking for local festivals and events that would not normally be found by foreigners - sometimes they are in the city, often they are smaller towns on the outskirts, like the Shibazakura Festival in the Mt Fuji Lakes area.

One thing for Kyoto - if you're not renting a car (something we now do every trip to avoid the madness of overcrowded buses), I recommend dividing the city into 4 quadrants and spending 1-2 days in each quadrant so you're not wasting time waiting for, or riding on buses especially those needing connections along the way. Keep the transfers short, walk more, and focus on one area rather than trying to zigzag around the city.