My trip hasn't happened yet, but already I've experienced some things:

Pros:
You can book waaaaayyyy more in advance than most hotels. Very helpful in planning to have your accommodations squared away so you can start figuring out what train stations to take, etc.

If your party is more than 3 (or even 3), it's wayyyy easier and much cheaper to do AirBnB. This price advantage increases exponentially the greater the number in your party. For families, AirBnB is a much easier and cheaper way to go. Obviously, the earlier you book, the greater your selection. So, if you book early, I'd say you get way more space for much cheaper than even "high end" hotels, particularly if your party is bigger than 2.

Since there are so many, you can really home in on the exact location you want to stay in. With the more limited selection of hotels, you may not be able to find a hotel in the exact location you want that will fit your party at a good price.

They typically give you step by step instructions on how to get to the place. With pictures. Incredibly helpful to someone new to Japan.

Cons:
The unexpected cancellations is a real threat. This alone may be enough to discourage some people to just stay at a hotel for peace of mind. My Osaka place has already been cancelled once. From this, I've figured out the person who has the AirBnB account controls a ton of listings. I think she's some kind of property manager. She hinted that the one I originally booked was cancelled cuz neighbors complained and she had to shut it down. This would be scary, except Osaka seems to have a TON of places that can accomodate my party of 5. I'm confident that even if I get cancelled last minute, that property manager can get me in someplace else (just might be in worse location and smaller). It's only a couple nights so worse case scenario, we crash at whatever hotel we can find. The other ones I've booked are the entire house (not apartment/condo/etc). Much less danger of complaining neighbors that way. Osaka and Tokyo right now seem to be in the most danger of having your AirBnB reservation cancelled based on news articles I've read. I'm ok in Tokyo cuz it's a friend's house (an actual house), even though he puts it up on AirBnB.

No hotel concierge. This means the luggage forwarding takuhaibin service isn't really available as there probably won't be any way for you to have your luggage accepted. Many AirBnBs have a local property manager who can help with directions, recommendations, etc. This makes up some of the benefits of a hotel concierge, but they won't physically be there.