Massey Ratings for MLS, built separately on goal difference by game, and expected goal difference by game. Those ratings are then used to calculate strength of schedule for each team, for their remaining schedule as well as for the games they've already played.
The 2016 MLS schedule used is from Matthew Bernhardt - https://gist.github.com/matt-bernhardt/9d1b276197159c48d0c0
Expected goal totals are from American Soccer Analysis - http://www.americansocceranalysis.com/by-game-2016/
An explainer and an R implementation of Massey ratings for the Premier League, from Martin Eastwood - http://pena.lt/y/2014/11/27/english-premier-league/
An explainer and a Python implementation of Massey ratings for basketball, from Scott Turner - http://netprophetblog.blogspot.com/2015/09/massey-example.html
Ken Massey's original honors thesis - http://www.mratings.com/theory/massey97.pdf