At the top of my head with some photos I was look back on and some links to get you some idea and some links. Hope this gets you started. For me I also spent time just walking aimlessly to some extend so .. some places abit harder for me to think where they are hehe.
Odaiba is like an oversize Suntec City + MBS + Esplanade.
(
http://www.japan-guide.com/e/e3008.html)
Giant Gundam Robot at Odaiba and get experience their Gundam Cafe if you are a fan.
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-9.JPG
Madame Trussard at Odaiba (Got to pay )
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-7.JPG
Mini Liberty statue at Odaiba
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-8.JPG
Odaiba Marine Park - Ferry Services ( you can use this to get to Senso-ji Temple by river on the same Anime ferry in the photo link below)
Jap manga inspired boat - Ferry service at Odaiba Marine Park (
http://www.deepjapan.org/a/974)
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014.JPG
History Garage(Toyota Megaweb) - Retro Car Musuem at Odaiba (
http://aroundtokyo.net/blog/history-garage/) -Free
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-10.JPG
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-12.JPG
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-13.JPG
Toyota Megweb Car Showroom. Largest I have ever seen. Like a car mart including some on display are sports cars, concept and racing cars..etc. -Free
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-11.JPG
Senso-ji Temple (Asakusa Temple)
2 Chome-3-1 Asakusa, Taito, Tokyo 111-0032, Japan
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-3.JPG
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-2.JPG
Tsukiji Fish Market
(
http://www.tsukiji-market.or.jp/tukiji_e.htm)
5 Chome-2-1 Tsukiji, Chuo, Tokyo 104-0045, Japan
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-5.JPG
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-6.JPG
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-4.JPG
Robot Restaurant (
http://www.shinjuku-robot.com/pc/ ) - Got to pay but worth it plus moderate dinner bits and drinks.
Robots, Blinding bedazzling techno colours and chicks, what's not to love?
Shinjuku, Kabukicho, 1 Chome−7−1
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-15.JPG
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-16.JPG
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-17.JPG (if you saw the movie Real Steel, you will recognize this robot as it was featured in the movie)
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-18.JPG
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-19.JPG
http://gallery.clubsnap.com/data/1046/medium/Toyko_2014-20.JPG
I would say use the internet to book as many of the tickets to where ever if you can then to do it while you are there. That is what I love about Japan. so advance and customer friendly services and ease of booking things in advance. This is better too as you have English text to read then to be there and trying to talk to them and make bookings. Not sure if you did that last trips you went but the internet has save me some problem with planning the trip.
Oh if you have not already done so, got to pay homage to the most faithful dog in Japan located at Shibuya if you know which dog that is. heh. There are others but I think you already have covered them. All the parks are just too beautiful depending on the time of the year. At the Meiji Park if you are lucky to catch a formal wedding taking pace it would really be fun to shoot shoot but stay respectful.
I can't wait for my next trip there to just spent time revisit all the places to do a proper walk about shooting session. Have a fun trip.
Ortega is a great expert given he has gone Japan a lot more then most folks I know. Have seen a lot of his trip shots on his Faceboy heheh He got his prize winning shot which also got picked up for the Nikon calendar from a trip he did not too long back. My last trip is about the same time as your. If it is sunny, the sky is so damn blue but it can change really quickly. I got some really good blue sky shots of Liberty for about a few hours and then it turn gloomy really quick and that was it. heh
So hope you get lucky with good weather to capture some really nice photos.