Going to a 16 game playoff would most definitely ruin the college football regular season. Those two games fish mentioned would be still be interesting, but wouldn't have nearly the implications as it currently does.
Now if the Big 10 and Pac 10 added a conference championship game, then I could see them going to an 8 team playoff where you have the 6 BCS conference championship winners, 1 wild card, and the last spot goes to the best non-bcs conference team. With that, these games would still have large implications in getting to your conference title game. And it would keep the non-bcs teams happy as one of them gets a title shot each year.