Actually, reading comments online, their youth system is a major problem right now. It's basically all rec soccer with crappy coaching and no skill development.
This article on TSN was a pretty interesting read.
Honestly Canada is a serious mess soccer wise. They're honestly at a point where the US was 30 years ago (at a point when Canada was about to qualify for Mexico 86), their Fed is run by a bunch of old guard soccer guys just seeking to further themselves and their buddies. There's no youth structure, no formal coaching programs, and their National Team is not good (even their Womens Team struggles more often than not, they preceded their Bronze Medal in 2012 with an 0-3 and out at the 2011 WWC).
Canada basically needs some real executive/management help before anything. They have tools to help them succeed player wise with 3 MLS teams and (soon to be) 2 NASL teams developing players. But they need real help organizing things. They named a new coach
two days before the Gold Cup! Their previous coach was fired in October! The biggest sign that things suck is that Vancouver and Montreal have their Academy Teams play in the US Development Academy leagues!
As for World Cup Qualifying, Canada is equal parts not as good and very unlucky. Since reaching the Hex in 1998 Qualifying (and reaching the Intercontinental Playoffs in 1994) they've gotten some pretty horrid draws in the Third Round. 2006 they had Costa Rica, Guatemala, and Honduras. 2010 they had Mexico, Jamaica, and Honduras! Their biggest fault is they lost a lot at home: 2002 they won one game at home, 2006 they tied one and lost two, 2010 they tied two and lost one, in 2014 they actually won two and tied one but that tie to Honduras cost them a spot in the Hex.
Canada is just a mess at the top and like they say, "* rolls downhill." The MLS teams I think engineering a hostile takeover of the CSA is about their only chance to be honest.