Well to add to some of the stuff here, it seems like you and I have similar interest especially for when I was younger, i.e. anime gaming, etc although I enjoyed the culture a lot too.
Disney: Disneyland is like any Disneyland in the world as they are meant to be for the most part with a little local flair and the castles usually being a bit different. If you are a Disney fan check out DisneySea instead much different, and IMHO more enjoyable for me, but I do say it's a bit more adult themed. The wife is a DisneyFreak so she just loves to go whenever she can, they sometimes have after 5 or 6 special tickets that are cheaper which lets you catch the tail end of things and the night shows. Also if you do plan to go, go during a week day it's MUCH less crowded and you won't be spending a lot of time waiting on line. We usually plan our route out and grab fastpass tickets while waiting to do other stuff. But for the last few times we've basically been able to go in and just hop on rides within 5 minutes. So like everyone says you're looking at a full day, unless you do the evening pass. From Tokyo Station it takes about 20 minutes to get to Maihama Station then Disneyland is right there or you can take the disney monorail 2 stops to DisneySea (about a 5-10minute ride)
Akihabara: Definitely as an Anime Fan, though given your short time frame I would only spend about 2-3hrs there but it can also be half a day. There are many stores and it has been becoming more of a Maid Cafe place. The backroads will have more technology stuff, but the main stores like Sofmap will be like Bic Camera or Yodobashi Camera, so I would steer clear of Sofmap's main stores. The only exception to that is Sofmap has 1 store that has just video games if you want to see that, you'll notice it because the store is mostly red and has about 6 37" screens int he front showing different new games. But other than that check out Animate for character goods (there is one at Ikebukuro's Otome Rd too), some of the stores up and down the road for more Models.
Odaiba: One of my favorite places. It's a great little island of rebuilt land, the monorail goes around but you'll probably get off at daiba stop. Aqua City is there with Sega's Joypolis which is a big arcade of sorts in a themepark kind of design. They just renovated it so I don't know what it's like now inside. Usually the wife and I go at nights for the night ticket. Driver City is a new mall opened about a few months ago. The Giant Gundam is outside still, and there is a Gundam museum and experience inside on the top floor near Round 1 Amusements (also a giant arcade but with more sports too). Most likely as well during the time you visit in December, FujiTV headquarters (unmistakeable building they have a HUGE steps, and what looks like a giant ball hanging in the middle of the building) will have some sort of winter special going on. Then if you walk across the pedestrian bridge that links one side of Odaiba to the other (or take the monorail for a loop around) you will see VenusFort. It's another shopping mall but it's like the Bellagio in Las Vegas with the painted ceiling like a sky and lights that change color to give it the feeling of sunrise to sunset. All in all you could spend about half a day to a full day in Odaiba seeing everything.
Shinjuku Gyoenmae: It's a large park and lots of natural beauty to it, and is also like a public garden. Unfortunately the timing of your trip again won't allow you to see it at it's full beauty since you're about 3-4 months early for the Cherry Blossom Viewing (Sakura Trees) and about a month late for the chrysanthemum blossoms. But it would still probably be a nice stroll in the park.
Ghibli Museum: Another of my favorites. You'll need to get tickets in advance for this. I'd recommend getting them before you leave here's the page with the info from Ghibli:
The official site of Ghibli Museum, Mitaka in Japan - TICKETS if you buy them when you arrive into Japan immediately find a Lawson to buy them there (they have little Kiosks, but they are all in Japanese). The museum itself takes quite a bit of time to get to as you have to transfer to a bus. Bring a good coat, gloves and bundle up much of it is outdoors. You're probably looking to spend anywhere from 3-6hours here depending on what you do.
Tokyo Sky Tree /
Tokyo Tower: TST was built to replace TT as a communications tower. I have not been up TST yet but I hear it is fantastic. TT i've been up many times, I love both the day and night views. if you want to get the best of both I'd suggest trying to get up before sunset. Though you'll have to time it since there are usually lines. TT I use to spend about 2-3hrs there including the time it takes to wait in line and go. I hear the lines for TST are still pretty long right now, but I'm not sure how the ticketing situation is, maybe someone will have more info on this.
Squenix Store: This is in Shinjuku so I'd spend time not just at the store but walking around, it's also very close to Harajuku which is know for their specific fasion. But here is a review of Squenix store if you haven't seen it already gives a pretty good account of what to expect:
The Square Enix Showcase: Shinjuku Japan | The Japan Guy
Sensoji Temple: is a great place as well, very crowded though. Lots of things to see in front of the temple along the ally that leads up to it. Enjoy the wagashi and all the other Japanese treats lined up. Oh and try out the Melon Pan that is here too, it's quite famous in japan, it's pretty big and tasty. Here's the website: sorry it's in Japanese Only:
ﾃ?ﾃｵﾃ?ｰﾂ｡ﾂ｡ﾂｲﾃ鳴ｷﾃｮﾃ?ｲ :: ﾃ?ﾃｵﾃ?ｰﾂｻﾃｻﾂ｡ﾂｦﾃ?ﾃｵﾃ?ｰ'ﾃ堕ｸﾃｷﾂ､ﾃ篠､'ﾂｵﾃ卍ｷﾃ?｡ﾂｦﾂ､ﾂｪﾂｿﾂｩﾂｻﾃｶﾂ｡ﾂｦﾂ､ﾂｪﾃ?堋ｻﾂｺﾂ､ﾃ擬/url]
Imperial palace: If I remember correctly you have to apply for tickets for a set time on this too but I can't remember. It's a very calm and quiet place and has quite a bit of history behind it. The imperial gardens are also nearby to take a look at as well. I personally go through these pretty quickly but you can probably spend 2-3 hours or more here as well.
So given the amount of stuff you want to do an the amount of time you have, planning is definitely needed. A lot of the places can be done rather quickly but to enjoy them you'll want to spend some time. Stores don't typically open until about 10am here so something like Squenix shop in the morning before you go somewhere might be a good idea. You'll want to get use to the Yamanote Line since that's where a majority of your places you want to visit are going to be on. For Odaiba you'll get off at Shimbashi station and go find the Yurikamome monorail, it's an unattended monorail so if you can get to the front of the monorail and you'll have a nice view of the ride as you take it towards Rainbow Bridge.
As for your initial planning it seems pretty good, you might want to put Odaiba on the first day too since it looks like the day you'll be running around Tokyo. I would also decide what to cut in case you end up staying at places too long, and then maybe having that as a backup for places to visit if you end up finishing early. Also you might want to look at the times for things too, i think the imperial palace and ghibli museum share the same hours and they are quite far apart so you might want to split those up. I mentioned earlier that shops open at 10am they close around 8pm as well, so places like Akiba and Otome you might want to do during the day. Odaiba still has quite a bit to see even with some of the stores closed at night, in Driver city I beilieve the stores close at 8pm as well, there is a Calbee shop that always has long lines. They are a famous snack brand here in Japan and they make fresh fries, chips and stuff.
I hope this info helps!