Honeymoon for Cherry Blossoms

Hello! We are planning a honeymoon to Japan, departing the US to Tokyo on March 20 and leaving Tokyo on April 6. As we are looking to book accommodations, transport, and ideally other must-do-in-advance reservations, I would greatly appreciate advice on how to prepare while at the same time remaining flexible as cherry blossoms will be impossible to predict.

We will definitely stay in Tokyo and Kyoto, with possible day trips. Since we are in Japan for so long, we also want to consider the possibility of staying in at least a third city. 

Stay in Tokyo (day trip or overnight to Kawaguchiko/5 Lakes to try to get Fuji views); will start and end in Tokyo, so can divide up sites and day trips (or just come back for a day or two at the end)

Stay in Kyoto (stay trip or overnight to Osaka; possible day trips to Nara, Himeji, Uji, Kanazawa, Ine)

We are very interested in seeing Kyushu, but understand this may not make sense to just visit one city/not have too much time or a car

Stay overnight in a ryokan (ideally not over-the-top expensive but with a private and/or mixed-gender onsen; I have seen some mixed thoughts on Hakone but would appreciate thoughts on locations)

Any other "less-touristy" cities or towns as day-trips or overnights; we do not mind lots of travel time and changing locations. We would plan to store our larger suitcases somewhere in Tokyo or Kyoto if we move around a lot.

I would greatly appreciate your thoughts on the logistics of some of this, particularly what/how we should book for cherry blossoms, since each city will have overlap with flowering and peak bloom. 

Additionally, one of us is a vegetarian (no seafood either) and one of us is not–I know there are apps and guides for vegetarian restaurants, but if anyone has a recommendation, particularly in Tokyo and Kyoto, for restaurants that not only have good vegetarian food but also have very good meat/seafood (including pork and chicken based ramen and sushi), I would greatly appreciate it!

by Unlikely-Employer-87