You make it sound like evaluating what the skaters do on more than one ice (aka, using more than one competition) means that the skaters didn't earn it on the ice. Not sure how that computes.
Let's think of it this way -- the World Championship is one competition. It doesn't matter if you won the GPF (Czisny, Chan, Davis White, S/S), totally dropped the ball during that one circuit (Mao Asada) or if you didn't go at all (ala Yuna Kim or Virtue/Moir). What matters is how you do those two programs during that competition.
The ISU won't be saying things like "Well so-and-so had a bad skate at Worlds, but they did so well at this other competition so they should get the silver medal instead of the other guy who had a great two skates but sucked the rest of the year."
I think this is where Mathman is going with all his comments about letting the skaters going for it on one ice. You know that Nationals is where you can win it or lose it. Then you should train accordingly and strive to be consistent.
Also one should considered that this luxury of "depth of competitions" is not available to those moving up the levels. Take Leah Keiser, for instance. She was the 2010 Novice champions, but ended up placing 6th at sectionals this year, and therefore, not qualifying for nationals this year. Yes, it's not comparable -- but I make this point to stay that outside of the senior ranks and junior ranks, most only have "one competition," one chance.
Also Johnny Weir isn't the only bronze medalist who was passed on after doing poorly at Nationals:
In 1990 Holly Cook finished 3rd, but managed to get a spot on the World team. She ended up being the second highest finisher with a bronze medal. But then she went and bombed nationals in 1991. No one thought for a second that Cook should go to worlds (or maybe they did at the time, can anyone remember?) instead of Kerrigan, who won bronze and who up to that point had very little international experience.
That said, i think the USFSA does allow for exceptions, but exceptions, like anything else, should only be used for the rarest of occasions and require some special cases. (i.e Nancy getting whacked in the knee; Michelle going to 2006 Olympics due to injury but required to do a test skate later).
The one thing I do find funny with the USFSA is how they choose their Junior Worlds team. Now that is a bit inconsistent. Why send someone like Agnes Z, who has been doing seniors? It makes sense to send Christina again because she hasn't moved up yet. But then again Agnes is still within junior level, so I guess you could make the case there.