Tokyo to Kyoto

Hello,
My group of 3 will be arriving at the Haneda airport in Tokyo on March 25. We’ll spend Weds. to Sun. exploring Tokyo and then travel by bullet train to Kyoto. We’ll explore Kyoto, Hiroshima, possibly Osaka or Hakone before returning by bullet train to Tokyo on Friday, April 3. We’ll fly home the next day, April 4. It seems like a Regional JR West Pass is a better value than a JR Pass. based on our region of focus. Am I correct? Do most visitors use the subway in Tokyo? Is there a subway pass to buy? If I purchase a Regional Pass, could you confirm which one covers me the most? (there’s a lot of options) Do I separately purchase a round trip ticket for the Shinkansen? It that permissible once in Japan, or do we purchase ahead of time?
Thank you so much in advance.
Stephanie