We decided to go with this package because we decided we could save a bit of money. Some warning though: do some research on what days you are traveling on the Shinkansen, beware of weekends and especially holiday weekends, the unreserved lines are long and hot in the summer, unless you are willing to stand. We tried to go from Tokyo to Kyoto on the Sat before Mountain day and it was terrible. Coming back on Wed afternoon was fine. Also plan out what you want to do for your subway/bus pass day to make the most of it. Will not cover going to Inari gates.