Playing time is/can be a issue even at those younger age groups, there were talking about this all week in the B2003 forum
http://glxy.ussoccerda.com/sam/teams/index.php?team=1654414
Between the two teams that played last week: 5 players not rooster-ed, 14 subs, two of which got into the game but the 2nd one only played 5 mins. Basically 17-18 players from two teams not playing that week. Yes there are 7 subs but about 0- to half of those are normally used and remember these is only 3 times plus half times that you can sub so multiple numbers would have to be subed to get 7 on which again doesn't happen much.
Subing for the last 5-10 minutes or only getting a 15 min start doesn't help players that much and what I've seen over the years my kid has been involved is players looking to move at the first transfer window due to lack of playing time among other things. The suggested playing time recommendations are just that and not guarantee of playing times, some follow those better than others.
The reports and audits the clubs receive sometime touch upon this and others times not so much but the stats are keep and the end of year totals can be interesting. The transfer process has a whole bunch of provisions that you can look up in the rules but if you don't have the 25% of time its a easy process but players may not train or otherwise participate with a Development Academy team that they are not officially rostered with prior to approval of a transfer request, that both team must agree to or if disputed there are other provisions.
The is also a sequence of Development Academy games that all clubs must conform to for example U-17/18 games must be played prior to U-15/16 games and b. U-14 games must be played prior to U-13 games. This makes adding 2nd teams to the mix highly unlikely simply not enough field space or time slots unless everybody is playing at complexes which they are not.