I was in Tokyo and Osaka last year, and I went to Tokyo, Kyoto, Osaka, and Fukuoka in 2009.
JR pass or night busses are the way to go if you want to see more than one city. Night busses are cheaper than the bullet train (Shinkansen) and are pretty comfortable for a nights sleep if you can deal with the occasionally slightly bumpy road/traffic noise. However, these issues are mild in Japan compared to Vietnam/Laos where I've also used night busses. Also, using a night bus saves you a night in a hotel if $$$s are an issue. However, consider taking a bullet train at least once too, because they're cool. (Don't be late) - That goes for all public transport.
Try a capsule hotel at least once. They're a thing, and they're cool if you're not claustraphobic or a very large person.
Tokyo is great; it takes 10 days minimum to see ALL of it properly, but you don't need to go that far. 3-4 nights will be sufficient. Plan and look up what you want to do because that city has IT ALL and if you plan to just wander around and see what you find, (you'll find a lot of great stuff!), you might miss out on something you'll regret not seeing/doing.
Kyoto is a 100% must see! It's pretty much central, it's beautiful, it's friendly and it's unforgettable. It's a reasonably small place (3 days-ish), but you may want to stay longer just to soak it in.
April is prime Cherry Blossom season, so you'll see some of that I'm sure. I was in Osaka in March and we found 1 tree that had already bloomed. That was special in it's own way, but when they're all out it must be a wonderful sight. Tokyo tree's tend to bloom first if I remember right (this may be artifically encouraged but I don't know).
Osaka is a cool town, but not essential I guess. That's not to say don't go. Decide for yourself.
GO to Nagasaki or Hiroshima if you have any interest at all in the history. It's not nice, it's heartbreaking, but you'll remember it and more importantly get a totally different perspective on the horrors of it. You can't understand it fully until you see the museums. I only went to Nagasaki, but I'll never forget what I saw. They're done very well.
Mt Fuji: Definitely get a look at it, and if you have any hiking experience, climb it. I did and WOW! It's not too tough, but you need to be prepared. I won't go into details here, but if you want some advice, I did a whole heap of research on it I can share with you. Just ask.Edit: My gf just reminded me that it's only open in the summer! Whoops!
Tokyo->Kyoto should be done back to back in my opinion. The contrast between the two is what helps to make Kyoto so memorable.
I'm certainly not the biggest expert on Japan, but if you want any extra questions answered, I'll do my best. Enjoy it!
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