The 'Protocol-Level vs Application-Layer MEV Mitigation' debate is a fundamental discussion about where to implement protections against Maximal Extractable Value (MEV) in blockchain systems. It revolves around the trade-offs between building MEV protection directly into the blockchain protocol layer, providing standardized and comprehensive protection, versus implementing it at the application layer, allowing for more flexible and specialized solutions. It addresses the balance between system-wide standardization and the ability to create tailored protection mechanisms for specific use cases.