by far.
1) More fans and market = byu, including national following. This is typically the most important thing. You think ESPN is going to pay an independent Yewt program as much as they would byu? Hades no.
2) Better tradition and national brand name = byu. this goes along with the first point.
3) Better overall teams = byu
4) Better basketball team = byu
5) Better recent football BCS = Yewts, though overall the football teams are pretty close record wise the past 6 years and own the same number of MWC titles.
6) Research instituion = both, and who cares.
You tell me what was the swinging factor to the point of which byu was never even considered? Has to be religion.