They aren't really phasing out the divisions. They are just renaming them. To quote from the minutes of the NCAA Division 1 Board of Directors August 1 meeting:
"In another action regarding the two football subdivisions in Division I, the Board approved new labels. The presidents approved a change in terminology to “Football Bowl Subdivision” for the former I-A classification and “NCAA Football Championship Subdivision” for the former I-AA group. The Collegiate Commissioners Association helped develop the new labels.
"The presidents believe the new nomenclature, which becomes effective in December, more accurately distinguishes Division I institutions for purposes of governing football, the only sport for which such a distinction is necessary. Members felt the old nomenclature inaccurately tiered Division I institutions in all sports, not just football, and produced instances in which media outlets and other entities incorrectly cited institutions as being Division I-AA in basketball or baseball, for example."
So the two subdivisions will still be there. They will just have different names to reflect the way they choose a champion.