Alps or Hokkaido for the first half of June

We'll be in Japan from the 1st to the 16th of june, arriving to Tokyo and leaving from Osaka.
We've already been to Tokyo and around, so we'll spend a couple of days there, 4/5 days around kyoto/osaka and the days in between spent either travelling around the japanese Alps or driving around Hokkaido.

Our first idea was doing the "traditional" route (Matsumoto, Kanazawa, Takayama...) but I'm afraid we'll be caught there in the middle of the rainy season. So, Hokkaido it was, but then you dig deeper and it's also supposed to rain there even if there's no rainy season.

Summarizing: Japanese Alps or Hokkaido from the 4th to the 11th of june

My vote goes to Hokkaido. Totally different from rest of Japan and many flowers should be in bloom.
But Alps is fine too but will be hotter.

I spent 16 days travelling in Hokkaido 2 months ago, the island is indeed fairly different from many parts of Japan. I love Hokkaido, have visited numerous times, and I would not hesitate to recommend it . June is also a good time to visit, be sure to get a rental car!

Rainy season does not affect the whole country for the whole month. As a regular frontal weather system at that time of year it moves south to north. You might get rain, you might not - depends on the season.

hard to get a hotel room but Yakasoi Soran is in Sapporo and something that you will remember the rest of your life. I have seen it twice