7 days Itinerary

We will be in Japan March 6 to April 1 (26 nights on the ground). Our plan looks like this: Tokyo 6 nights, Nara 1 night, Kyoto 6 nights, Koyasan 2 nights, Miyajima 2 nights. We then have a choice that we are pretty stuck in making: Kanazawa 4 nights with Takayama 3 nights before training back to Tokyo for 2 nights OR Okayama, Matsue, Naoshima and ? Both areas are interesting to us but wondering if weather and logistics make the Okayama choice a better one for the last week in March. Thanks for any input, we really are stuck!

I think the question is of you want to see Sakura or not. Last week of March often othe early beginning https://www.japan-guide.com/e/e2011_when.html
So you might want to keep some flexibility in your plan. Note that Sakura when they are just opening arenft a very impressive sight. Ifd say that from about 70% they get some spectacular.

Without Sakura, both your ideas are fine. I personally didnft like Takayama, however on my 2 months trip by bike it was the first and probably only place overrun by tourist. So that had a bad influence on my judgement. However if you compare it to Kyoto itfs not overrun at all.
http://bicycletraveljapan.blogspot.com/2017/10/day-30-takayama-sightse...

I personally really like the inland sea. And maybe Ifd drop Matsue for Takamatsu (on Shikoku) instead, which has a lovely garden and you can visit some temples on Shikoku. But I also liked Kurashiki, Bitchu Takahashi and Inujima. And when I went a few years earlier Naoshima and Teshima.
http://bicycletraveljapan.blogspot.com/2017/11/part-9-day-44-47-okayam...

I could probably spend a week or more only in that region. But I could also spend a week in Kanazawa, Noto peninsula, Takayama and Hirayu onsen area.

Enjoy planning your trip to Japan!