Otherwise the big brands will always be selected to play in conference championships. I remember one year the Big 12 had Oklahoma, Texas, & Texas Tech all tied with each other and that conference looked to the BCS poll at the time to solve their tiebreakers which was very controversial. The problem is the conferences are so big teams often don't play each other. There were multiple 6-2 teams. Duke struggled in the non-conference portion of their schedule but they were one of the best ACC teams. The Blue Devils have a very good QB who was actually Tulane's QB last season (now Tulane has the BYU QB from last season). The teams in the tiebreaker only had 1 common opponent which was 3-9 Syracuse and they couldn't do head-to-head because they didn't play each other. Also there is no guarantee Miami would have won the conference championship game even if they were selected. If it was Miami vs Virginia then the ACC would have at worst the 11 seed and Tulane would get the 12 seed instead of James Madison.
As far as James Madison I think they probably deserved to get it. The selection committee already stacks the deck heavily against the mid-majors (compare where the G5 teams are ranked in the AP & Coaches poll) but ever since joining FBS James Madison has over an 800 winning percentage and before that they won 2 national championships at the FCS level. They probably deserve to get in more than Tulane but the American conference is a lot tougher than the Sun Belt. Normally I would root for Tulane but I don't like their QB so I'm rooting for James Madison though I wouldn't mind if Indiana won it all as they don't bother me like the 5 star brands. Also rooting for Texas Tech as the representative of the Big 12.
I think they should either keep things the same or expand the playoff while still giving conference champions a shot. The fact they meant to give at least 1 G5 team a shot keeps me interested in the sport after Arizona State is eliminated before the selection committee does their final ranking which is often. As far as the ACC that looked like a conference that no one really wanted to win.