Travelling alone gives more freedom on choosing the lodging. It all depends on your needs, as well as location. There are so many choices, minshoku, minbaku (AirBnB), capsule, business hotels, hostels, apartments (both short and long term; however shortest usually not fewer than 5 nights), onsen hotels, normal hotels and highend hotels.
The first question would be: what is your budget. I, for one, will never stay in hostels and capsules. To me, security and comfort would be paramount. When I walked whole day outside I need a comfortable bed and room to rest and sleep.
For my solo Tokyo trip 2 weeks' back, I booked AirBnB in Shibuya/Shinjuku area. First time staying and found it to be very enjoyable as you got to meet others from different cultures (One from USA and one from Isreal) and breakfast in the morning could be interesting. Also chatting with host is also enjoyable. And the pricing is just 1/3 of what we have paid for a hotel with ultra small room nearby (NishiShinjuku) a while back.
For my other solo trips (not in Japan but in various countries), I have stayed in hotels of various grades (3 - 5 stars) and found that for a solo traveller, we do not need a very big room as long as the bed is comfortable (at least a queen size) and with proper hot water for bathing. I have stayed in suites before and I found it to be not required cause you don't even utilise the space.
That's just me cause I will put my budget into good food instead of super nice rooms