IMO, Kyoto is real nice, if you're into a lot of the Japanese cultural stuff (i.e. temples, castles, etc).
Well, to answer your first question, to get around Japan in it's entirety, I think you'd be safe with the Shinkansen.
As for transportation in Tokyo, their's the extensive, complicated "subway" system of Japan. Yes, they do offer Romanisized translations, Just be sure to NOT take the trains around 11pmish, as that's when office workers get home, and you have to wait in a human line so they can literally haul you and cram you up inside the carts. Don't worry, you won't get robbed. :laugh:
Tokyo's subway system should grant you access to all the places you want to see, whether it be Harajuku, Akihabara, or even Nippori (small, quiet Japanese town). Oh yeah, and if you get lost, ask the Japanese officers in their little office box thingie (a Koban, IIRC)
As for Kyoto, they have large green buses on hydrolics. Sometimes they're full, othertimes they're dead empty. Yes, if it gets to that point, you will be standing and holding on to either the railing or the hanging loop above, so make sure you don't have much on your hands when riding in any Japanese transportation vehicle (even Tokyo's "subway"). I'm pretty sure that most hotels offer an All Day pass for ~$5 US. So if you know exactly where you're going, buy that. As long as you don't get off the map (and no, IIRC, the Nintendo headquarters is not on there), you should be safe. Don't worry, the Hotels should have this map.
As for anywhere else, you could use a taxi or something. Not real familiar with other methods of transportation elsewhere. Oh yeah! If you have access to a bike, that would help. Or speed walking.
So to sum up:
Tokyo - "Subway", should get you everywhere, check map and study it, ask directions from Police officers in the Koban. Pay attention to colors on the map. The pricing ranges from how far you travel, or I think you could get a pass or something.
Kyoto - Use the city buses on hydrollics. Their not hard to miss. If you miss one, run to the next closest bus stop. Don't worry, you'll make it there before the bus does. And if you're worried about which trains to take, you can go to Kyoto's bus station. It's real nice, and all the buses eventually meet there.
Anywhere else - Walking, Bike, or taxi. I was on a tour bus, but that's different.
From one city to another - Tour bus or Shinkansen. Logically speaking, avoid going from one city to another, as the Shinkansen is rather pricey.
Feel free to ask more questions. I can answer to the best of my ability, but I can't guarantee exact answers, since I don't live in Japan, I have only visited Japan once, for 9 days.
