The southern division will have six teams and the two northern divisions will have five teams each.
Stoke, Tottenham, Fulham and Birmingham have decided not to participate. Arsenal was considering withdrawing, but finally decided to stay.
Fulham academy director Huw Jennings, who once headed the Southampton academy that produced Theo Walcott and Gareth Bale, said: "The system is well organised up to under-18 level but the reserve programme is not fit for purpose and the clubs have been voting with their feet."