Adeno-associated virus (AAV) is widely regarded as a leading vector for gene therapy, underscored by clinical successes such as Luxturna and Zolgensma. However, efficient gene delivery to hard-to-transduce tissues—including the retina, deep skeletal muscle, and the central nervous system—remains a significant challenge, limited by structural barriers, preexisting immunity, and dose-dependent toxicities. This review systematically outlines recent advances in overcoming these delivery bottlenecks. We delve into four key strategic areas: (i) capsid engineering (e.g., rational design, directed evolution, and computational approaches) to enhance tropism and evade immune detection; (ii) innovative delivery routes (local, systemic, and physical/chemical methods) to improve vector bioavailability; (iii) modulation of intracellular trafficking to boost nuclear delivery; and (iv) immunomodulatory strategies to mitigate both innate and adaptive immune responses. We further highlight translational progress in neuromuscular and retinal diseases and discuss persistent challenges. Looking forward, we envision that the convergence of next-generation capsids, smart vector systems, and integrated delivery platforms will be critical to expand the therapeutic landscape of AAVs from rare monogenic disorders to broader clinical applications.
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