Half way through the CONCACAF Champions League now, and while Seattle has essentially been eliminated the FMF continues to dominate. MLS sides though aren't as bad as they've been, and at this point two sit in second.
Group A - Cruz Azul (6 pts, +6 GD), Real Salt Lake (6 pts, + 3 GD)
Now Toronto FC has the points (3 so far) that they could salvage their non-League season, but it is unlikely they make such a run. Arabe Unido is likely done. Their flopping and fouling won't succeed in a Group Stage. If TFC does rise up it will only be at RSL's demise, but Kreis isn't likely to let that happen. He has lead some to believe that CCL is more important than the MLS Cup.
Group B - Santos Laguna (7 pts, +4 GD), Columbus Crew (6 pts, +3 GD)
Municipal with 2 points is highly unlikely to make a run, and a 1 point Joe Public certainly doesn't have the talent. This Group is essentially over and MLS with the Crew will likely advance.
Group D - Toluca (7 pts, +7 GD), Puerto Rico Islanders (4 pts, 0 GD)
Yes, the USSF Division 2 team has managed to compete with a lower budget for salary and travel than the Seattle Sounders. They already beat the LA Galaxy. They are doing it with tactics, not talent. And they do it often enough. Olimpia does sit with 4 pts and a negative 2 GD and could threaten the low budget former USL side. FAS with 1 pt and -5 differential is likely done.
Group C - Monterrey (9 pts, +5 GD), Saprissa (6 pts, +4 GD)
Seattle Sounders sit in last with zero points and tied for third worst goal differential (-5). Marathon's position is decent enough that they could make a run, if they were any good. They don't seem it though.
But let's note, of the teams in second after 3 of 6 rounds two are MLS sides, and one is a USSF D 2 side. They have similar or smaller budgets than Seattle. Similar or worse travel as well. Of the 3rd place teams with a decent shot (TFC and Olimpia) they also small budgets for salary and travel. They actually won games though.
Getting beat by Monterrey wasn't the problem. It was the poor performances against Marathon and Saprissa. Teams with minor budgets who Seattle should have challenged. Seattle had larger rosters than both, and likely a larger total salary. Seattle also had more World Cup caliber players.
While the CCL now likely becomes a showcase for the "B" team, let's not pretend this was due to roster limitations or travel considerations. It was purely because of the performance on the pitch. Other MLS teams dealt with the same problems, got wins and will likely advance to the knockout stage.