Choose the main bases
Nearby cities can be day trips; they do not automatically need separate hotels.
Tokyo, Kyoto, Osaka: familiar names, different bases. Choose the shape of the trip before filling every day.
Compare a focused regional stay with a trip that changes regions.
Kyoto, Nara and Osaka form a regional trip with different emphases: temples and gardens, Nara’s historic sites, and Osaka’s food and city life. Choose a main base, then decide which places deserve their own nights.
These are route shapes, not a day-by-day schedule. Your arrival airport and onward flight should help set the order.

JNTO advises limiting long-distance moves on shorter trips. Once you know your bases, compare the actual train journeys before deciding whether a pass is useful.
JR Pass prices and a Tokyo–Kyoto ticket comparisonNearby cities can be day trips; they do not automatically need separate hotels.
Compare where you enter and leave Japan with the first and last base.
A city IC card and an intercity rail ticket solve different parts of the journey.