Have you attracted bigger recruits since leaving the MWC? Have you received more donations from big time donors? Have you improved fan excitement? Are gameday ticket sales up? Are you beating Utah?
It doesn't seem to me that Independence has achieved any of these goals outside of perhaps scheduling more marquee games against big opponents that you didn't used to play. Now, you could say that winning fixes everything and as long as the team starts winning, all those things will change. But I think your current schedule with 5-6 "power teams" sets you up for perpetual mediocrity in terms of your finishes. It's really doubtful that you ever run the table with that type of schedule given your recruiting restrictions. Are fans ok with basically 6-9 wins every season for ever and ever? Because I think that's what Independence and your current model gets you.
If you found a conference, you could still schedule 1-2 juggernauts or big teams per year in addition to Utah and then win 10-12 games during your solid seasons and make better bowl appearances, win conference championships and achieve player awards and accolades, develop more rivalries and interesting storylines, etc.
Just some thoughts from an outsider