Additions to itinerary

We will be in Tokyo for 15 days from 11/15-11/29. I've already planned 90% of the trip, but still have a few open slots--any recommendations? We will be staying in Shinjuku the entire time.

Note that we've already visted Nikko/Kamakura/Hakone last time, so didn't include it here.

15-Nov Shinjuku
16-Nov Ueno Akihabara
17-Nov Mount Takao Shinjuku (dinner)
18-Nov Ikebukuro
19-Nov Shibuya
20-Nov Asakusa Odaiba
21-Nov Meiji-jingu Gaien + Harajuku+yoyogi park Yebisu
22-Nov Kawagoe
23-Nov Mount Fuji/Lake Kawaguchiko (day trip)
24-Nov ShinYokohama Yokohama (MM21)
25-Nov Imperial Palace (Opens 9am,Close M+F) Roppongi/Tokyo Midtown
26-Nov Kichij Shimokitazawa
27-Nov Shinjuku Gyoen "Koishikawa Korakuen
"
28-Nov Rikugien Autumn leaves ???
29-Nov Ginza Hama Rikyu ?

Ikebukuro is just about another urban centre, which I don't think require to spend an entire day there. Perhaps u can combine it with Shibuya or another place along the JR line.
If u enjoy Hayao Miyazaki's animation works, do visit Studio Ghibli Museum at Kichijoji.
As u have already covered Hakone/Nikko/Kamakura, perhaps spend a few days away from urban Tokyo to Nagano or Sendai.