Phenolphtalein is lacking an -0- bridge which induces rigidity in fluorescein, this rigidity prevents rotation and loss of absorbed energy via this mechanism, resulting in the need for fluorescein to emit photons in the visible range of light. Phenolphtalein can easily lose energy via this mechanism in non visible regions. This means that fluorescein has a much greater fluorescence yield than phenolphtalein.
Also worth considering is the pH you're utilising, at high pH phenolpthalein can degrade to the In(OH)3- ion which reduces conjugation across the molecule and eliminates the push pull system created by electron donating O- and the electron withdrawing acid group
attached a publication comparing the two compounds by Boguta and Wrobel
I am also in accordance with Dr. alex. Both this two molecule present in two forms. One is lactoide and another is chinoide form. But the oxo-tricyclic ring present in fluorescein play the key role behind the higher fluorescence quantum yield.