Tokyo Sky Tree will be open by then. It will be the tallest structure you'll be able to see from in Tokyo, if not Japan.
TOKYO SKY TREE
When I go to Japan, I tend to stay in hotels with a rate higher than $100/day, so I can't help you there....
As far as places to go, you can go here and see:
http://www.japan-guide.com/e/e2164.html or here:
http://wikitravel.org/en/Tokyo or even here:
Japan National Tourism Organization | Find a Location | Tokyo | Tokyo
There's a lot of information out there....