Some options (I like lists):
Super 2 Breakaway
1. In-conference playoffs with champions playing for the title
2. Top teams (#TBD) set up cross conference tournament, open with something like B1G#1 vs SEC#4, etc.
3. Just seed top # of teams across the two conferences into a bracket
ISSUES: Who are they going to play in the regular season? In-conference only?
Could the outsiders develop a playoff that competes for attention or casts doubt on "True" National Champion?
Form a new NCAA Division above D-1
1. Super 2 Champs are the only ones to get a autobid. Rest are at-large (mostly Super 2s and a couple tokens from lesser conferences).
2. Same as above, but a 3rd conference champ also gets an autobid (likely a merged ACC/B12 or the last survivor).
3. No autobids. Again, most of playoff lineup will be Super 2, plus whoever the hot outsiders are that crack the rankings in a given season.
ISSUE: How would the selection system vary from the current one?
Does anyone care who wins the FCS? Is there ever a question if North Dakota State is the true D1 champ instead of the FBS champ? The same thing would apply to a new sub division of B18 and SEC teams. Their playoff will determine their champ. Even if the AP poll chose the FBS champ as #1, the P2 champ would say isn't that cute and not care. They got their NCAA trophy and got paid.
Does most of the talent (including coaching talent) end up in FBS or FCS? So if the B18 and SEC broke away into their own sub division, they would have all the talent (even worse than now). What kid or coach would want to be in the lower division (like with FCS vs FBS)?
Most likely they would go to 10 game conference schedules and 1-2 OOC vs the other conference. Then instead of an FCS game like they have now, they have one FBS cupcake game.
The left behind FBS teams would have no marquee Ws. Clemson can go undefeated but if their biggest Ws are FSU and BYU why would anyone think they are better than the P2 sub division champ. Same as with North Dakota State winning the FCS.
As to Part II
The B18 and SEC cannot dictate how the FBS playoff goes. The ACC, B12, and G5 need to agree to the system. It is why the G5 was thrown a bone in the new system. The B18 and SEC have all the power and will absolutely get a favorable outcome, but they cannot close out the rest of the FBS. The PAC going away isn't going to change the playoff from 6 conference champs to 2.
I think they could push for more playoff teams and/or no auto Top 4 as conference champs. Maybe something like...
Top 3 conference champs make the Quarterfinals.
Next 3 conference champs and 3 best at larges make the 2nd Round.
Bottom 3 conference champs and 5 next best at larges are in the 1st Round.
That gives every conference champ a shot. There would be 8 at larges (only 6 currently) which will be mostly B18 and SEC teams.
For example...
QFs: UGA, Michigan, Clemson
2nd Round: K State, Tulane, Troy, TCU, Ohio State, Bama
1st Round: UTSA, Fresno State, Toledo, Tennessee, Utah, USC, Penn State, Washington
That would have yielded:
5 B18
3 SEC
3 B12
1 AAC, ACC, CUSA, MAC, MWC, Sun Belt
1st Round
10. Tennesse vs 17. Toledo
11. USC vs 16. Fresno State
12. Utah vs 15. UTSA
13. Penn State vs 14. Washington
2nd Round
4. TCU vs 13. Penn State
5. Ohio State vs 12. Utah
6. Bama vs 11. USC
7. K State vs 10. Tennessee
8. Tulane vs 9. Troy
QF
1. UGA vs 8. Tulane
2. Michigan vs 7. K State
3. Clemson vs 6. Bama
4. TCU vs 5. Ohio State
SF
1. UGA vs 5. Ohio State
2. Michigan vs 6. Bama
CG
1. UGA vs 6. Bama
All the CG game money goes to the SEC. All the SF money is split between the SEC and B18.