As with everything else, the question is which league will be perceived as #1 by players/parents. My guess is that the theory for non-MLS teams is that if the best players go to the MLS academies and players want to play against the best players, even if only to get a chance to be scouted by those MLS academy coaches or by the D1 coaches who scout the games in the MLS league, then they'll be willing to play for the non-MLS teams in that league.
ECNL is probably better for the clubs in terms of league organization and stability, being able to determine your club's own fate (since clubs have a seat at the table and there won't be MLS teams that run the league to benefit themselves) and making it easier to keep your own players. Whether that translates to benefits for the players is not as clear. HS play is less of a draw for boys than girls, but it might help with some kids if the MLS league doesn't allow it or plays through it. There might be more organized college showcases for ECNL teams too since MLS is less likely to care about that (although MLS does still place a lot of players in D1 schools every year and they retain their rights and sometimes sign them as homegrown players).
The real question will be how the MLS league treats the non-MLS teams. If the non-MLS teams only get limited games against the MLS teams to provide local scrimmages and otherwise just play against themselves, that will probably get old fast. Even then, for players the tie to the MLS academies may be enough to differentiate the league from ECNL and other local options.