Nobody said that the current situation is fair. Most people (including myself and I would say the vast majority of posters here) see all these inequities with the BCS.
But bear in mind the BCS has a relatively brief history. Before the BCS (or Bowl Alliance that preceded it), EVERYTHING was driven by polls. It was highly unlikely that the #1 and #2 would meet, since their conferences were typically locked into deals with different bowls.
PAC and Big-!0 - Rose,
WAC - Fiesta,
Big 8/12 - Orange,
SEC - Sugar,
SWC - Cotton,
Eastern Independents (usually Penn State would go to Orange, Sugar, Cotton)
Notre Dame (would not go to a bowl before early 1970s, went to Cotton a lot)
ACC - generally not highly rated in football before FSU came aboard - Peach
Arguments abounded. People had issue with the polls. Bowl match-ups were often lousy.
Big Ten #2 and lower from the Big Ten could not go ANYWHERE. There was an exclusive spot for the champ in the Rose Bowl. PERIOD. And often the Big Ten "champ" was not the best team in the Big Ten. If there was a tie, the team to have gone the longest without an appearance got the slot.
When PSU was independent, Paterno had back-to-back undefeated untied teams in 1968-69 and 1969-70 IIRC, both won the Orange Bowl. With the pollsters always having a bias that East Coast football stank (at times it did OTHER than PSU), Penn State got no consideration.
It's happened 4 times to Penn State during the Paterno era, most recently in 1994 right after they joined the Big Ten and CLOBBERED everyone in sight with Kerry Collins, Ki-jana Carter, Kyle Brady, Joe Jurivicious, etc., scoring 50 points a game. Nebraska did roughly the same thing and they were locked into separate bowls. A potential for a great game was missed. So we argue....
At least now there is a system to pair #1 and #2. However, how we arrive at #1 and #2 (polls) still stinks. Probably the ONLY way to arrive at a championship that everyone can agree on (in my opinion) is to include everybody and anybody with any claim, and decide it on the field.
I think 16 teams (if the NCAA runs this, bylaws state there MUST be at least 8 at-large berths). So say the champ of the top 7 conferences gets in, and any other undefeated champ is GUARANTEED an at-large, regrdless of rank. Most of the at-large slots would go to the "power conferences" and that is OK, however the key is to NOT DISCLUDE any undefeated team. So if Boise St. (WAC), Utah (MWC), Ball State (MAC), Tulsa (C-USA) all "run the table" they get in.
Then it's all decided on the field, using a seeded bracket. If you lose to anyone, you are out, no complaining, any losing means that you are not the best team.