In the last year alone, travel to Japan went up 150%. This means that somewhere down the line there are going to be more hotels, more restaurants, and more travel services available, but for now, there's just a higher demand for what's already in place. Therefore, it's never too early to plan your trip.
We're not just saying this because we're a travel company. We're saying it because we get lots of inquiries 3-4 months before where there are no hotels available in places like Kyoto. They're popular destinations, and depending on the time of year (especially cherry blossoms and fall foliage), you might find yourself disappointed in the options available to you for hotels and air tickets. Air tickets and hotel/ryokan reservations can be made a year before, and it is highly recommended to plan as soon as you know you'll be traveling.
Museum tickets and events, guided tours, geisha/cooking/sumo/traditional arts experiences etc. can be booked closer to the time of your travel, but the earlier you can book these, the better. Reservations for certain restaurants should be made further in advance than others, but those definitely can be decided later.
At the time of this post, if you were to check any popular online travel sites to make hotel reservations for cherry blossoms in 2016 in somewhere like Kyoto, you'll see it's almost completely booked. Since lots of hotels have a completely free cancellation system (not all!), so you can actually make those reservations before you've even decided on a flight- just read the fine print and the cancellation policy.