Nature / Weather, Tokyo
How exciting Tokyo might be, the biggest metropolis in the world is indeed clean but if you look at what's in the air this does not apply. Admitedly, it is not as bad as in Mexico City or Cairo, but smog is an issue in Tokyo. This probably annoys asthmatic as much as it annoys tourists, because only in winter when the air clears up Mt. Fuji is viewable from the many high-rise buildings of Tokyo. So do not expect to see far during summer time. Anyway, I like Tokyo, nonetheless.
Avoid June/early July and September for the rain. June/July is infamous for being called the "Rainy Season." They receive numerous short to heavy rains despite the fact that it's near the start of summer. September is bad because Japan is ravaged by some fierce typhoons. My keitai died once during a lightning storm.
For winter avoid January - March. Those periods can be exceptionally cold and can snow. Trains can be packed and the roads are really slippery. My hand froze one morning walking up the stairs while holding onto the railing after a night of snow.
August also is a nasty month as the temperature can be exceptionally humid. Although subways and stores may be air conditioned, expect to sweat (and stink!) a lot.
July to November is Typhoon season, you flight and schedule might be changed simply by the strong winds and rain happen. Besides, train and other transportation might stop as well. Make sure that you have some loose schedule before and after your journey to Japan.
The typhoon season in Japan is August to October but the months of June and July is classed as the raining season.