I'm going to Japan this coming autumn with the family (me, husband, 18yo & 16yo). Was BA the optimal choice? Not exactly, but if I wanted to use BA Holidays + GUF to travel in J I had to adapt, also because we are constrained by the school holidays dates.
Sometimes one has to choose between savings and convenience.
We are planning 3 nights in Kyoto and 2 in Tokyo. We can't do more with the time available.