Two weeks sounds good. I wouldn't spend more than two days in Tokyo. It's pretty overwhelming.
I'm assuming you two have bought your Japan Rail Passes.
Imperial Palace - easily walked from Tokyo station. Tours only on weekdays at 10 and 2, so get there early to get your spot on the tour. The East Gardens are closed on Mondays and Fridays, so ideally the best day to come would be Tue, Wed or Thur.
Tokyo Metropolitan Government Center has the best free views of Tokyo, open as late as 11PM. This is in Shinjuku.
Ghibli Museum, buy your tickets ASAP at any Lawson's chances are they're already sold out but it's worth a shot.
http://www.lawson.co.jp/ghibli/museum/ticket/detail/english.html
Meiji Shrine in Harajuku is probably the most beautiful in Tokyo. dat giant torii gate. Also a good chance to walk around with your gf undisturbed by others in the woods.
Don't forget to take a picture of the Hachiko statue next to Shibuya station.
http://www.gojapango.com/tokyo/shibuya_hachiko_statue.htm
Sumo wresting. Luckily for you, you'll be in Tokyo at a time when the Grand Slam Tournament is happening, from the 13th to the 27th. More info here:
http://www.gotokyo.org/en/tourists/topics_event/topics/120903/topics.html
Eat at a maid cafe in Akihabara just for the hell of it.
Tokyo's a very walkable city, just walking and wandering around aimlessly can be good enough.
Most importantly, work with your girlfriend on where she would also like to go. I know she's leaving it all up to you, but it's important to make her feel like she's contributing to the itinerary - this is her trip, too. fake edit: oh she lived there for a few years well nevermind she's got it down
This is all excellent advice.
Seriously, spend as much time as you can in Osaka/Kyoto and get Tokyo out of the way as soon as possible. I would have recommended going to Sapporo as well if you were going in early February instead of September, but alas.
Akihabara should be the last place you'd want to buy games at, but if you really insist on it limit your game-buying there to only games that both you really want and are sure will be hard to find elsewhere. When buying games in Japan, my general rules are: always check stores further away from Akiba and then work your way in, always check the Book-Offs first, then check the smaller game specialty stores (like GEO), and larger electronics stores like BIC/Yodobashi are very good for new releases. From what I've seen, used games seem to be cheaper in Osaka than in Tokyo.
Akihabara is good for other things though, mainly the arcades. Be sure to visit the Try Tower, the Taito Hey, and the Natsuge Museum. There's also a tiny videogame-themed bar called A-Button in the area that's nice to visit (and their food is decent). Since you're going with your girlfriend, I'd recommend having a snack at an Akiba maid cafe called Schatz Kiste (
http://schatz-kiste.net/ ), is a very high-brow maid cafe with various books and board games available to use while you're there. Or if you'd rather visit a more "traditional" one, I'd recommend one called JAM.
While you're in Tokyo, you should stop by Nakano Broadway, which is essentially Tokyo's 2nd Akihabara. It's an indoor mall located directly in front of Nakano station and right through the Sun Plaza. It's full of shops catering to just about ever nerdy hobby you can think of. There's also a really good bakery in the Sun Plaza called Bon, and I highly recommend buying some bread there to snack on (should be on the right side of the shopping street if walking in from the station). There's also some good restaurants in the side-streets on the right, including a good/cheap pizzeria called Napoli and a nice spaghetti place that I forgot the name of, just ask around and you should be able to find them in no time.
Another fun thing to do while in Tokyo is to take the train to Takaranobaba station and take pictures of the large murals dedicated to Osamu Tezuka, which are located directly in front of the station. The famous Mikado arcade is also around the corner from the station, and is loaded with competitive arcade games, but mainly versus fighters.
Now onto Osaka...
Osaka castle is a beautiful sight, especially during the evening when the whole thing is lit up. Den Den Town, Osaka's Akiba, is also worth a visit and is a very good place to do some videogame shopping. Of course, walking through the entire length of Doutonbori is something that must be done, it's also worth crisscrossing through some of the streets that intersect it. The Book-Off in the area has a basement full of older games at good prices. Relatively close to the famous Glico Man sign, there should be both a great Mexican restaurant and a great Middle Eastern restaurant fairly close to each other. Osaka is also the best place to go bar-hopping, you're bound to meet lots of nice and interesting people while doing so.
Unfortunately, I have yet to visit Kyoto, but I know there are a lot of nice places to visit there.