The original Big 12 was just mismanaged badly. The worst thing they did was the football schedule / division alignment. It essentially made the North schools non-existent in the big Texas media/recruiting markets and consequently damaged their per-team value. I think it was hard to envision it playing out that way when the league was formed - with Nebraska and Colorado so strong - but it was dumb not to adapt when the obvious became obvious a decade in.
By the early to mid 2000s, there should have been discussions within the league about rearranging the divisions on the basis of something other than geography.
OU, Texas,, BU, KU, KSU, OSU
NU, A&M, TTU, MU, ISU, CU
Something like this ^ would preserve most rivalries and it would distribute media/recruiting exposure more evenly for all 12 teams in the conference's big markets. Big 12 1.0 had the North schools basically invisible in DFW and Houston during football season. None of those schools were part of the conference standings that mattered (the South standings.) Under a different divisional alignment, you probably also get support for the cross-division rivalry game that was working really well in the SEC. The Big 12 left money on the table by not having OU play Nebraska every year. The Huskers might have been less willing to jump ship if they were actually playing their only real rival every year and getting more exposure in Texas, too.