In 2000 they became an independent and have since had a serious strategic advantage over their opponents.
Conference wins and losses are much more important than out-of-conference losses. A team can have several out-of-conference losses and still win their conference, but more than one or two conference losses all but dooms a team from achieving their goals and any recognition outside the conference.
Navy runs an unusual offense in the form of the triple option, a running based attack and they rarely throw more than 5 or 6 passes a game. It requires more practice and game-planning to teach linebackers and corners the new assignments and how to "stay-at-home" in a zone rather than just pursuing the ball as they usually do.
But a loss to Navy is not nearly as bad for the opponents because they are out-of-conference. Hence, less game planning, less emphasis in practice, and less year-to-year focus because they are less likely to repeat against opponents more than two or three games.
Why would a coach spend more than a few practices preparing against Navy when he is more important offenses and intra-conference opponents coming up?
Well, I don't think he would. And that's why I think Navy has an inherent advantage in college football by being an independent.