It's a very human reaction to want to change the rules in response to a recent disaster (not that losing 1 spot is that much of a disaster). For many upon many years, the US was the only federation that consistently scored 3 spots for men at Worlds. The system worked great all those times, I don't think it's wise to chuck it out one time it didn't.
The system has always been bad. Skaters should qualify for Worlds based upon their OWN international results (each country can decide who gets to go to Four Continents and Europeans, which would be important qualifiers) and entries should not be limited to a maximum of 3 per country to begin with.