Our decision to stay 12 days in Tokyo was met with pretty much the same reaction as our decision to stay 10 days in Taipei. Everyone was like, "What...won't you be bored? What's there to do? You can finish Tokyo in 3 days!"
I personally think you can't really say you know a place just by visiting the places listed in Lonely Planet or TripAdvisor. Part of the process of getting to know a place is really just sitting still while the world moves by, and absorbing every movement every sight every sound, smell and texture; understanding why the people in that city do the things they do; not making judgment on them using the standards from which you originate from; not experiencing the city through a Selfie stick. You definitely cannot do that in 3 days.
We stayed at a very nice Airbnb apartment at the end of Harajuku. The owner, Makiko, was super nice and prepared so many things for us - including free Wifi egg, bicycles and a restaurant list. Although we did not meet in real life, but she definitely played a big part in making this trip such a nice one. We really did very normal things like taking out the trash, cooking meals, doing laundry - things you wouldn't typically do on a vacation. But you see, we really wanted to experience living in the heart of Tokyo. And live we did.
We did not plan anything on the itinerary, save for a few meals with friends...oh yes and DisneySea! Of course I had a few places I wanted to visit in mind, but it was like one place a day? And the rest of the time we just enjoyed the process of getting there, wandering into small alleys, stopping to eat at random cafes and restaurants, having fun getting squished on the trains, getting lost in translation, huddling close while it rained, skipping together when the sun came out. Simply being.