1) AAC and MWC exit fees are a complete non-factor.
2) BYU has a reputation of "not playing well with others" which will persist as an independent but could be worked on in a conference.
3) As an independent, BYU has guaranteed visibility, whether the performance is good or bad. In the AAC/MWC, a team can slip by sort of unnoticed in a down year, but will still get the same level of attention in a good year as an independent BYU.
4) Better bowl options, including a much better shot at an access bowl appearance.