Mobile applications (apps) have grown into complex, multi-platform systems that support diverse services and operate within varying regulatory and distribution contexts. Traditional analysis techniques have established a strong foundation for ensuring quality, security, and compliance, but face increasing challenges as mobile apps evolve. This article presents a three-layer perspective to examine these challenges. The Artifact Layer highlights how heterogeneous code bases and protection mechanisms reduce the analyzability of packaged apps. The Runtime Layer addresses growing execution complexity, from multi-modal interactions and super-app architectures to AI-driven autonomous operations. The Ecosystem Layer considers broader contexts, including emerging platforms, fragmented distribution channels, and region-specific regulatory requirements. New characteristics across these layers interact and compound, creating difficulties that existing approaches are not designed to handle. For each layer, we identify key challenges and potential research directions, including framework-aware analysis, adaptive testing, and policy-aware compliance verification. We also discuss how large language models bring new analytical capabilities to the field, while their integration into apps raises new security and privacy concerns. This article aims to clarify where established methods fall short and highlight directions for future research in this evolving field.

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