I have a brother who's a senior at Navy, so I have followed them pretty closely. The one thing that always strikes me is how, oftentimes, the coaches they are playing against them scheme very poorly - especially on the offensive side of the ball.
For example, yesterday, Gary Pinkel consistently stuck with the outside routes, even when Navy began playing 2 DE's and essentially only 5 guys in the box. Pinkel appeared frustrated and hasty the entire game... which is entirely the wrong way to approach playing Navy. Pinkel had the inside run open almost all game and for some reason, refused to go for it. If the inside run had been established, the outside pass would have been so much more open. I believe that too many opposing coaches have the philosophy: "Let's get up on Navy early, so that they have to play from behind." While it is clear Navy struggles playing from behind, it makes the opposing coaches far too aggressive during their gameplanning. Stick with what Navy gives you, don't let them bait you into what's not there.
As far as stopping that offense - I have played against the triple option, but I don't pretend to be an expert in the field. However, tackling is so, so important against them. The offense can't be stopped all the time, however, because they have more plays per series than most teams, you have more chances to stop them as they march down the field.
Beyond scheming, though, I can never believe how "frustrated" opposing coaches appear during the game. For heaven's sake, you are a head coach. I understand if you are angry, but if you look frustrated and at a loss for what to do, your players are going to reflect that in your play. Coaches like Lou Holtz and Nick Saban are terrific against teams like Navy, because they respect the offense of Navy and preach extreme patience to their players. You have to know it's going to be a long game going in, and there will be frustrating times.
I was especially thinking about Kelly coaching ND next year against Navy, during the game. At first, I was very worried by how Navy's D was effectively stopping the spread, and how they were ripping apart a mediocre defense. However, after watching Pinkel, I became more confident in Kelly, because it is all about player commitment with him. I think that his leadership and demand for patience and team unity will force players to play smart, and to "stay home and read their keys."
Anyways, sorry for the long post... guess we are all bored waiting for after the Sugar Bowl to hear our staff announced.