Was in Tokyo for a week at the end of July, best experience I had... Fantastic food, people are so polite, the subway system is freaking amazing (cheap too) and Akihabara felt like I died and went to heaven.
I highly recommend going to Tokyo Skytree and the nearby Shrine, best of old and new Japan.
Also the NEX discount is only from Narita to Tokyo, going to Narita is 3000 something yen.
The site has an updated timetable that was very useful since we were staying in Shibuya and not every NEX stops in Shibuya station.
If the GAF Meet-up ends up happening after Sept 8th, I could give you a free entrance ticket or two if you want since I got a few of those for being a TGS exhibitor.
Also, should we make a new thread for the meet-up with Evilore, or can we use this one to make the arrangements? I will be arriving on Sept 8th, and will be available on both weekdays and weekends until Oct 8th, except during the TGS (from the 17th until the 21st of September).
We stayed in a hotel near Miyajima and bought a combo ticket that was shinkansen + hotel for a reasonable price (ymmv). Also means only 3 hours on the train each way rather than 5.
We arrived in Hiroshima around lunchtime, then headed down to Miyajima in the evening (after okonamiyaki in Hiroshima) and stayed in a hotel right next to the ferry. Next morning nice and early on the ferry, across to the island - did the shrine area and up the cable car, then back across on the Ferry, up to Hiroshima station and back to Tokyo. The miyajima bit took pretty much a whole day including getting back to Tokyo, but we were with our kids so didn't arrive back late.
If you were willing to get to Hiroshima really early, and get back to Tokyo really late, then it might be possible in one day but you'd be rushing around which is kind of opposite to what you want for that area IMO.