Family trip for 4

Hi, we would love some advice please!
We are a family of 2 adults and 2 children (they will be aged 13 and 10 at the time of travelling).
Our 3 week itinerary is:
Week 1: arrive in Osaka - flights to Sapporo (Niseko)
Week 2: flights to Hiroshima (to visit Miyajima island) - Kyoto (with side trip to Nara) - Nagoya (Legoland) - Nagano (Shibu onsen)
Week 3: Fujigawaguchiko - Tokyo (Ueno) - Osaka
Is it better off buying individual tickets for each train ride? If so, can I still reserve seats online, as we will have 2 pieces of big luggage, or will I need to do that once we arrive in Japan?
Thank you so much for your assistance.
Kind regards,
Liza