Consider buying
JR passes. No need to figure out fares when travelling on the JR lines, and of course, unlimited travel for duration of pass.
Saga's suggestion: to purchase
a rail pass JR Suica, and also PASMO (non JR) within The Greater Tokyo area. These cards' value can be topped up.
TOKYO
Places to visit
Omotesando, Aoyama - little cafes and cool shops
MidTown Tokyo: 21_21 Design Sight, Precce supermart, Suntory Museum
Roppongi Hills: Mori Museum
Kanda: Isegen
http://www.isegen.com/English/ankou/ Places to stay
Hotel Monterey Ginza, Ginza Itchome (near Harry Winston bldg) - clean, most necessities, near Yurakucho Station (7 to 15 mins walk, depending on how much you're carrying..)
Andon Ryokan. I like room 28 - near stairs and washroom. View of sky and willow tree. (about 12 mins walk to train station)
Note: I like reading reading reviews at
Trip Advisor.
KYOTO
Places to visit
KiyomizuderaArashiyama
Places to stay
New Miyako Hotel Just across from train station with many shops and restaurants. Free shuttle bus to sister hotel Westin Miyako in Higashiyama Hills, so can walk to Nanzenji (one of my favourite places), Higashiyama, Philosopher's Walk.
NAGOYA