Shinkansen

Pros

• You can take the Shinkansen between Tokyo and Kanazawa and then continue onto Kyoto. I did this last May.
• Shinkansen is around ~ 2h 20min If this is your first time in Japan I would recommend to stay the whole time in Tokyo not travel for half day/day trips.
• Not sure the cost difference between bus from Tokyo to Osaka vs Shinkansen but Shinkansen will take you there in less than 3 hours so it’s worth considering the time savings.
• True. And Shinkansen as well.
• Day 4 Tokyo - Shinkansen + teamLab + Odaiba

Cons

• Shinkansen may be questionable between kagoshima and hakata. ... There was an earthquake. It's not currently running.
• Probably depends on the bag size but anything much bigger than our carry ons would have hung over. They definitely would not have fit large checked bags (much smaller than what airlines consider "oversized").
• The mistake I made during my booking was I booked Delhi-Tokyo-Delhi coz it was Rs 7k cheaper than Delhi-Tokyo, Osaka-Delhi. But later realised that coming back from Osaka to Tokyo needs Shinkansen which is ~Rs 8k itself. So ended up doin...
• I would highly recommend staying in Tokyo for the 5 days. Seems like you will only have one full day in Kyoto, incidents and conflicts may eat up some of your time especially during shinkansen travel.
• Shinkansen is a little pricey, but only needed for rather long distances.