My s/o and friend visited Japan in 04 during golden week, a year later I visited it during the same time.
It was a nice vacation, laid back, everything seemed to be open (except for a few stores which had the whole week off) but the major attractions were typically open.
Last time I went during x-mas and new years unfortunately many things I wanted to see or do were closed due to those holidays.
We took subways, taxi's and the bullet train during golden week, travel was not bad. New Years is the worst travel time as everyone goes back to their home town (usually heading away from Tokyo however.)