I am helping my parents plan a family trip for our family of 5 to Japan. We want to take advantage of Spring Break and plan to go March 13-21 (that includes flight days). We have a 12 year old with us, everyone else adult age.

Our plan is to fly into Tokyo and stay there til Thursday the 17th (~3 whole days) then head to Kyoto by bullet train on Friday the 18th. We would spend the weekend in Kyoto before heading back to Tokyo Monday the 21st to catch our evening flight home.

I would like some advice from experienced travelers though, since we've never been to Japan. I mostly have questions on transportation, but any advice or tips on must-sees is greatly appreciated.

We're flying into Narita and plan to take luggage, one piece per person.What's the best way to get to our hotel in Tokyo?Saw the NEX and bus options, but with luggage I don't know what's the best option.perhaps NEX To Tokyo station and then taxi to hotel?

Is the 7 day Rail Pass worth it?
We would use it for the Tokyo-Kyoto round trip mainly. We are considering going to Mt. Fuji on one of the Tokyo days. I know we could use it on NEX, but I'm scared that if we activate it on Monday the 14th it'll expire before we can use it for our trip back to Tokyo the next Monday, the 21st.

Is Mt. Fuji worth it? Or are there better things to see?

Are the green cars good for taking luggage?I know it might be a pain so I'm trying to make it as easy as possible to travel with our luggage.

What are absolute must-sees you recommend?

I appreciate any advice or suggestions. Total noob to Japan here so I don't know what the travel environment is like. I'm excited though and can't wait to get there!