The following is some information I picked up through experience, was a little passage that i wrote to a club where he was at a loss as to what to do with so many players.
A recent development that I witnessed was a restructuring of an academy. Presents several challenges, including accommodating a massive range of abilities.
It is scientifically proven that players with similar ability will progress more quickly, avoiding a sense of intimidation. If you are provided with the opportunity to separate the players into groups, ensure you avoid using words like elite and development and so on. This I have found has a detrimental effect on players confidence despite their varying abilities, suggestions I would say to you would use shirt colours or I have recently seen clubs using reoccurring European words like Milan, Rovers or Wanderers.
The third team can become a bit of an experiment for you, If you are still enjoying an influx of players this can be used as a platform for football, an experience perhaps for younger players to experience of being part of a team, to experience pitch side environment and the right attitudes to show. You could use this team as a sort of exhibition group, send them to be part of tournaments, training abroad. then you could use it as a platform to recruit further players.
More and more we are seeing some basic coaching drop in sessions, effectively this is used simply for people to get a taste of football without the pressure and intimidation of other experienced players, something that it proven to be a productive concept.