"Tailor-made" is a worn-out phrase. It means very different things depending on who's using it, so I'd rather show what it means when I say it.
A fifteen-day trip I designed this year begins in Tokyo, at a hotel facing the Imperial Palace moat. Three nights. It's the most conventional possible starting point, and it's chosen on purpose: nothing is scheduled on the first day. Thirteen hours of flying and a 7-8 hour time difference aren't solved by willpower, and a guide waiting in the lobby at nine the next morning guarantees the first visits happen at half strength.
From there the trip grows more intricate, in a good way. Tsukiji Market and a private sushi workshop. A dinner with a sumo show, which is touristy and fun, and there's no need to pretend otherwise. A tea ceremony with a master who doesn't just prepare it, but explains the etiquette while preparing it, which is where the difference between attending and understanding lies.
From there to Hakone, to a ryokan with a private open-air bath. Two nights. And then five in Kyoto, which is what it takes: Kyoto with two nights is a list of temples, and with five it starts to become a city.
The trip ends on Mount Koya, sleeping in a Buddhist temple. Not a hotel styled like a temple: an actual temple, with a tatami room and vegetarian food prepared by the monks. At dawn you pray with them, then have breakfast. Two nights.
That contrast — the five-star hotel facing the Imperial Palace and the monastic room in Koyasan, with twelve days in between — is exactly what I mean by tailor-made. It's not choosing between package A and package B. It's that the same trip can start in one place and end in its opposite, because that particular couple was going to be more drawn to the second after having gone through the first.
What doesn't show up in the itinerary is how much work it took to decide the order.
If Japan has been on your mind, write to me and I'll tell you when's the right time to go.