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Performance evaluation of hybrid (heterogeneous ISA) computing systems faces three major challenges: hybrid execution, multi-tasking, and system-level simulation variation. To evaluate system-level design decisions, a metric must encompass all forms of execution in a system, and incorporate any overheads introduced by hybrid execution. Differences in relative application speedups in a multi-tasking system complicate overall system performance evaluation. In full-system simulation, the relatively limited time-span for feasible tests compounds the evaluation problem. This paper discusses these challenges and presents metrics that address them.