It's surely the ending the season in California bit, because they have a like minded institution less than two hours away in Evanston, IL and that stopped being an annual affair after 1976. They've played Duke eight times, Vanderbilt three times. Feels like Stanford had their fun against ND during the Kelly Era and barring last year's pothole this series began to get a lot more one sided in ND's favor. That being said, Lou lost to Stanford in 1990 and 1992. I think with the "new era" of college football, Stanford is going to have some struggles and finding another Harbaugh/Shaw type run is going to be hard.
As a fan, the value of playing Navy drained for me years ago. It's really a no win situation in terms of the optics (ask Weis and Kelly), and if you're really that concerned about ND being a national brand, playing the service academies isn't exactly a badge of honor nationally. The road game typically happens in an NFL stadium or Ireland now anyway, if you're into traditional college football with games being played on campuses. Whatever debt ND owes Navy has been paid and then some as far as I'm concerned. Probably not the most popular thought for the traditionalists, but whatever.
They could drop both Navy and Stanford, and I'd be completely fine with that. The tradition I want them to recreate most is championships. It doesn't matter to me who they have to play and defeat in order to get there.