Instead of Maggie Walsh, Phil Coulson is put in charge of the Initiative during the events of Buffy the Vampire Slayer. Coulson's team (as of the end of Agents of S.H.I.E.L.D. season 1*) also come along for the ride. They do not bring any S.H.I.E.L.D. gear with them.
How does this change affect the Buffy-verse?
*
How does this change affect the Buffy-verse?
*
Except that Fitz is not brain-damaged and Coulson is not affected by 'alien weirdness'