Ideas for someone’s who already been

Okay, here's my deal.

I'm a person who's been to Tokyo multiple times, so I've seen all the usual stuff. I have a three day stopover in Japan, from 5/25 to 5/27, I arrive early in the morning on 5/25 and leave late at night on 5/27, so I'm counting it like I have 3 full days.

I have a rail pass and on the 26th I'm visiting a friend and his family in Nagoya. So that leaves me the 25th and the 27th. I really would like to see something new or different in Tokyo, or some place that I could get to easily by shinkansen. I've already been to Osaka, I haven't been to Kyoto, and wondering if one day there would be worth it. I'm also thinking of maybe seeing the Ghibli museum.

I'm interested in what people have to recommend. I can speak Japanese pretty well, enough to hold conversations, ask directions, order food, etc, but not fluent. So I'm not afraid of going off the beaten path if it's interesting :) Thanks for any advice.

Depends on what kind of attractions you are interested in. Here are some suggestions:
http://www.japan-guide.com/e/e623a.html

I donLt know if youLve done this; but thereLre two places in Odaiba I love; one is the onsen there, which is quite funny and kitsch; and the other is the Emergence and Innovation Science Museum (best museum in Tokyo IMO). If you like hiking you can go to Mount Takao, 50 mins. by train from Shinjuku; which has some nice paths to walk through.

What about a walking tour of Yanaka & Nezu area.(starting at JR Nippoi Staion) This was one of the only areas not bombed in WW2, so it has many old houses, temples, etc near the old cemetary area.

It's a very pleasant walk!!!

Sorry, typo error, that's JR Nippori Station.

Perhaps something in this would intrigue you: http://www.hellodamage.com/tdr/travelguide.htm

In a weird twist of fate, after I touched down in Tokyo I went to visit my friend in Nagoya, and his family insisted I stay there the entire time instead of staying in hotel :X

I got to learn a lot about Nagoya :)

I will take everyone's wonderful suggestion for next time