Absolutely! Your trip to these historically rich and culturally significant Japanese cities will be an exciting one! Here are some tips to ensure your experience is smooth:

Best Time to Visit:
Spring (March-May) and Fall (September-November) are generally considered the best times to visit these areas in Japan, as the weather is usually most pleasant and the scenery is beautiful.

Route and Accessibility:
You can reach Kyoto and Nara by train from Tokyo. From Kyoto, Koyasan can be reached by train and cable car while Ise can be visited via bus or train.

Altitude and Acclimatization:
These areas are all located at relatively low altitudes, thus acclimatization is not a major concern. However, do give yourself time to rest when you first arrive, especially after a long flight.

Accommodation and Booking:
Booking accommodation in advance is highly recommended, especially during peak seasons. There are a variety of options, from traditional ryokan inns to modern hotels. Koyasan offers the unique experience of shukubo, or temple lodgings.

Clothing and Essentials:
Due to weather changes, layering clothes is advised. Comfortable walking shoes are essential due to the amount of walking involved in exploring these regions.

Health and Safety:
Japanese cities are very safe. Nevertheless, it's a good idea to have travel insurance in place. Don't forget to bring any required prescription medicine and a basic travel health kit.

Local Etiquette and Respect:
Be respectful of Japanese customs and traditions. When visiting shrines or temples, follow the local customs - these can include washing your hands and mouth in the purification fountain, avoiding walking in the center of the path (reserved for deities), and bowing at the entrance.

Finally, remember that public onsen (hot springs) often have their own etiquette to follow including showering thoroughly before entering the water and not wearing bathing suits in most cases.