Planning a 14 night stay in Japan

HI all.
I am planning a trip to Japan Mid May for 2 weeks.

First of all I am really excited to be seeing Tokyo as I love technology and want to visit ALLOT of second hand stores for Retro nintendo sega etc.

Can someone please recommend a good place to stay that is close to all the action in Tokyo?

I also want to visit Akihabara and Den Den town.

Are they a far distance to get to?

I want to go to Kyoto and visit all the old temples and shrines , is Kyoto easy to get to?

Also is it worth visiting Osaka? Should I make my return flight back from Osaka if it's worth visiting?

I think 2 weeks should be a good enough time to see Japan.

Any recommendations would be much appreciated!
Theme parks roller coasters etc.

I would be more than happy to get on some good guided tours too. Ones that pick you up from the hotel etc.

Thanks in advance!

It's a good idea to choose a hotel that's a walking distance from a major subway / railway station. Yamanote line in particular is convenient for getting around the city. I guess Shinjuku would be one of the most happening places in Tokyo, but you could even stay in Akihabara if you'd like. It's conveniently located on the Yamanote line as well.

Kyoto and Osaka are right next to each other. It's easy to get there from Tokyo and travel between the two. There's more detailed information on the Kyoto and Osaka pages here at Japan Guide.

Den Den Town is in Osaka. You can walk there from the nearest Osaka Municipal Subway stations. I seem to remember seeing plenty of second hand games at the Mandarake Grand Chaos store, which you might want to visit even if it's not located in Den Den Town.

If you spend the first week in Tokyo area, and the second in Osaka and Kyoto, it'd make sense to fly into Tokyo and out of Kansai International Airport if you can get a good deal on the flights.

In addition to the big theme parks (Disney, USJ), there are plenty of smaller and less famous theme parks in Japan. Fuji-Q Highland is famous for its roller coasters, but I haven't been there personally. I thought Yomiuriland in Tokyo suburbs was nice. Themeparkreview.com has a lot of trip reports that are fun to read.