I completely understand. We first visited Japan in 2009. On our most recent trip a couple of weeks ago, it was almost like visiting an entirely different destination due to increased tourism. Some destinations were just ridiculous, like the Golden Pavilion which has apparently become a tourist trap where everyone now follows a narrow path around part of the lake only and constantly jostles (if not outright pushes and shoves) their way to taking photos.
The monkey park also really surprised us. On our first visit, the monkeys well outnumbered the tourists. On our most recent visit, it was definitely the other way around and it was disappointing to see so many tourists flaunting the clearly communicated rules of behaviour (e.g. not crouching down, not antagonising the monkeys, not feeding them outside of the "feeding pen").
I'm hopeful that Japan will be able to adapt to the increased tourism and still retain the many qualities that previously made it such an awesome place to visit. We will definitely be skipping Kyoto on future visits. Although, there are still wonderful experiences to be had (e.g. we visited Fushimi Inari late at night and there were very few people and the night-time views from the lookout points were lovely).
To manage your expectations, Tokyo Disneyland and DisneySea is now obviously very popular with foreign tourists and that does mean seeing some ... unfriendly behaviours in the parks.