I’ve spent considerable time in Tokyo in recent years as well. It’s largely the same as it ever was. “Incidents” with tourists are clearly blown out of proportion by local social media. Yes, there are visibly more foreigners than in 2008 (mostly immigrants who work and speak Japanese). No, the character of the city has not changed.
On my Shinkansen from Kyoto to Tokyo most recently, a noisy quartet of drunk guys chatted loudly for over a hour on the late evening weekday train and spilled a beer. Can you imagine the horror? They were Japanese restaurateurs from Osaka.
It’s not ridiculous, and you are relying purely on your anecdotal experiences to attempt to say otherwise. That is fine, you have every right to do that - but it does not negate the litany of media in English and Japanese that has covered this issue.
I also lived in the country for years, and am back several times a year to see friends and do business. I am fairly confident that the current situation and reputation that Kyoto has is not overstated; I do not know a single local who will even bother going at the moment.