My guess is that Oregon, Washington and maybe Stanford end up in the big 10. Same with Clemson, FSU and Miami to SEC. At that point, the two conferences will have so many solid teams lots of schools won't see the need to schedule ND.
Even if ND can still put together a solid schedule, which for the relatively near future seems likely, the politics will definitely encourage the 2 super conferences to focus on all the playoff spots going to their teams. With the current 4 teams playoff we will get frozen out a lot. At 6 or 8 teams, also likely. At 12 to 16 teams we would actually have an advantage as the super-conferences beat up on one another enough that a 1 or 2 loss ND would probably be pretty safe. Also, with super-conferences, recruiting will eventually suffer as kids want to play in the big leagues.
Mid to lower tier teams in the super conferences will become virtually irrelevant except for picking up nice checks from TV contracts. Mid to lower tier non conference teams will be even more irrelevant unless the win the last round of musical chairs to get a spot in a super-conference. Maybe the left outs create their own mega conference filled with teams like Boise State, Arizona, Arizona State, Washington State, Baylor, Kansas State. etc. That might be enough to get them a seat in the playoff if it expands to 16.
Be interesting to see if the super conferences go the pro soccer road with relegation.