Even after travelling to Japan a number of times (I can't even remember how many), there are still things I'm discovering to make life easier.
Lawsons convenience store has drinkable coffee. Family Mart convenience store has these drip coffee things (like a little box that you sit on your cup and pour water through). I'm not saying these options are the best ones out there. I'm not saying it's great coffee. But, in a dire pinch, it will get you through. There are many other convenience store coffee options but these are pretty much the only ones that won't have you wanting to pull out your taste buds.
Takkyubin! It's amazing. I've raved about takkyubin before -- you take your luggage to your hotel desk or the desk at the airport or even a convenience store and it gets delivered for you. No lugging it on overcrowded trains or through stations were no one will get the fuck out of your way and there is no elevator. But, even better, you can get delayed delivery. I'd always suspected as much but could find NOTHING on any of the web sites.
So, what does that mean? If, for example, you flew into Tokyo for a week then had a week of travelling around -- a night here and a night there on your JR Pass -- before heading to say Kyoto for a week or so, you could pack a small bag for that week of bumming around while getting your main luggage shipped. You travel free and easy.
Easy Airport Access
I discovered this by accident but, if you stay at a reasonably priced hotel,make sure it's near a more upmarket, fancy hotel. That way, instead of struggling through multiple train changes to get to the airport, you can just walk the half a block or so to the fancy hotel and catch the limousine bus to the airport.
Note: you can look on a map or transport planning app and think your route to the airport is going to be trouble free but more often than not, when you get to the subway station you can have a pretty darn substantial walk between the stations (up to a km). Similarly, your accommodation might be "near" a subway but a 2 minute walk to the subway might mean a 2 minute walk to the subway station entrance with a significant walk underground to the actual platform.
As i've mentioned, after my Airbnb experiences in Tokyo, i'd not use them again unless I knew the place was okay - ie. that it had been recommended by someone I trust or I'd stayed there before. It's unfortunate, because I do like having a whole apartment, but I don't want to experience turning up to a place to have it significantly different to the listing on the site (and filthy) again.
For longer term stays of over a month, I've found Sakura House really good and would definitely use them again. For shorter term, I think a hotel is the best option. My sister and I are thinking about picking one reasonably priced hotel chain (our last stay was at APA and we really liked them but there are others like Toyoko Inn) and signing up for their loyalty program so we get all the advantages.
Oh, and one small but important thing about Japanese hotels -- make sure they have year round airconditioning! I've stayed at a few places that turn the airconditioning off in winter and my room has gotten unbearably stuffy and hot.