Shinkansen

Pros

• We splurged for the Shinkansen which Google Maps did not even suggest: it was an excellent call.
• Subways were my main way of getting around and I used the Shinkansen when I moved from Osaka to Nagoya and then to Tokyo. Keep in mind that you can board any later train if you miss yours (unreserved seats only though), and if you have a...
• The shinkansen is expensive because you're paying for comfort and speed. I'd rather pay the extra money 😅
• Shinkansen - now, this is my experience. No need to buy in advance. Simple as that. They run every few minutes out of Tokyo. It's more like a commuter train than an airline ticket so no you don't need to be there 30 mins before.
• i think i will likely consolidate the Tokyo hotel and stay in one place, but the train from Osaka to Tokyo is actually a desired thing and not just a means to an end.

Cons

• I think a train to fukuoka would be better, since shinkansen takes quite a bit of time and will be pretty expensive.
• Personally I would not do an overnight bus. The bullet train is like 100$ USD for reserved seating iirc. And it's comfortable (I can't sleep on overnight buses so that may be my bias).
• It doesn’t happen often but when there are delays/issues with the Shinkansen it can cause massive delays or just stop the system completely. Happened to me in my last trip when getting back from Osaka to Tokyo was delayed by 5hrs.
• I hate dealing with heavy, large luggage on the Shinkansen.
• I've been in the situation where I've just barely missed a Shinkansen at Himeji, and it was quicker to take the Special Rapid rather than wait 40 minutes for the next Shinkansen.