Complex sentence: Being incredibly intelligent, she is one of the top students in the class, having entered U.A. through a scholarship, although despite her appearance, she has a self-esteem issue due to, in her mind, never being able to prove her own worth.
Split into simpler sentences: Being incredibly intelligent, she is one of the top students in the class, having entered U.A. through a scholarship. Although despite her skills, performance, and overall appearance, she has a self-esteem issue due to, in her mind, never being able to prove her own worth.