I think the main reason the triple option works for mid tier teams like Navy and Georgia Tech is precisely because they are mid tier teams.
The teams they play spend (I'm exaggerating) 5 minutes preparing for this offense. 99% of those two teams opponents see more traditional (spread or pro style) offenses for most of the season.
When teams prepare anymore for a spread offense, I'm sure they plan a base defense and stress what the responsibilities are against the triple option for just that week. That is precisely why those games are viewed as "trap" games. Games that should be won on talent alone - but blow one coverage or gap responsibility and it can be a major problem.
Also the increased speed at which defensive football is played takes away some of the big run threats from this type of offense. It's a lot easier to recover from a mistake than it used to be.
Its interesting to me that one of the most traditional offenses of the game is starting to be viewed as a novelty.