As an ALT I have seen some pretty badly run English programs in the school(eg I turn up, and they have no idea what class they want me to assist with, or leaving me for hours without work to-do - I generally try and make worksheets, lesson plans or extra material for the students to read around the subject matter, but that very rare gets used at some places.
I have even been at a school where all the English teachers were on holiday, no one really spoke English in the school and had no classes for 4 hours. It can get a little depressing.
But other English programs are amazing, one of my current schools I have written at least 40 pages of material to assist the students/extra study(voluntary), and they have informed the students, who contacted me directly for copies of that work. (I wish I was at this schoolfull time!).
After this programme was found to be not having much of a positive effective, the government decided to double the number of teachers they ship in from other countries.
I think they could improve English education in a number of ways: Either train up the teachers from abroad more thoroughly and give them a chance to stay much longer or send all Japanese people who teach English to study abroad for a extended period.
Edit: auto-correct glitches