Mystra is afraid of Gale.
Mystra is afraid of Gale because she knows that he is already more powerful than she was when she became Mystra.
Mystra is afraid of Gale because she knows that piece of Netherese magic should have, by all rights, killed him. And yet, somehow, he is still alive and while significantly nerfed by it, he is still fighting to save the world from the fate of becoming an Illithid playground at most of his ability.
Mystra is afraid of Gale because once a Chosen, always a Chosen and even she does not have the power to unmake it. It's how Ao shackled her to keep her from becoming too powerful. She intentionally keeps her distance from Gale to keep him from realizing this because he is easier to manipulate by emotion than to control by force.
Mystra is afraid of Gale because she knows the depth of his devotion. She knows what lengths he is willing to go to, what he's willing to sacrifice- not for Her- but for magic. That he has consistently kept her tenets despite his exile and perfectly embodies the qualities of one entrusted with the Weave. And because she can die and Ao has already reassigned her powers once.
Mystra is afraid of Gale because, like all of her Chosen, he can defy her. But as long as he respects and protects the Weave- if he calls upon it, she is bound by divine law to answer.
Mystra is afraid of Gale because she knows she has already bollocksed this Absolute thing up by letting it get control of the Crown of Karsus. That's why she tasks Gale with destroying it rather than trying to take it back for her. Because they are the only threats to her power. And if Gale ever realizes this, he is ambitious enough to try to overthrow her. She's already lost her ability to manipulate him with love and so her only recourse now is to keep him feeling so worthless and guilty that he never looks outside of himself for the source of his misery. Because nothing will humble a capable man faster than his own ego.
Mystra is afraid of Gale because his power is more valuable to her with him dead than as her liaison to the realms. Elminster is her people person. He's her PR guy. When Chosen die, their powers are absorbed back into the Weave to be siphoned until such time as She decides to re-embody them into a physical form wherein they once again have free will. And Mystra is only five years off of being fully restored to her godhood by Elminster, another Chosen whom she has cowed and cuckolded to keep in his place as loyal lap dog.
Mystra is afraid of Gale because if he doesn't destroy the Crown and Raphael uses it to unite the hells and enslave the kingdoms of men that his army could very well overthrow the outer planes- to which he has access within the House of Hope- both by using them to fight and to simultaneously cripple their power by revoking their faithpool. And gods in the dnd universe REQUIRE human worship for their existence and power. Another gift from Ao to keep them hobbled.
Mystra is afraid of Gale because he seeks to be her equal.
Mystra is afraid of Gale.