Tosfos in Pesachim asks why do we not use Besamim in Havdala which is recited in the Kiddush on Yom Tov which immediately follows Shabbos?
Rabbi Frand answers by quoting the Avnei Neizer who states that there is a Neshoma Yiseira on Yom Tov and therefore we do not smell Besamim in Havdala after Yom Tov? Since the Neshama Yiseira does not depart after Yom Tov, therefore there is no need for the Besamim. Unlike the Neshama Yiseira which comes on Shabbos without work on our part, the extra Kedusha on Yom Tov requires that we work to prepare for it. Since we have earned this Kedusha, it does not depart when Yom Tov ends.