The objective of this paper is to discuss unresolved research issues when linking the literatures on efficiency measurement and the design and operation of engineered systems. I focus on five themes that have emerged in the last decade. These include: engineering system design, resilience and sustainability of infrastructure systems, physical and behavioral representations of disaggregated subsystems, messy data, and the dynamic characteristics of engineered systems. I also provide an initial conceptualization of key yet interrelated issues within each of the themes. Along with the themes I suggest existing modeling formulations in the efficiency measurement literature (DEA, network DEA, fuzzy clustering, and the Dynamic Productive Efficiency Model) that serve as an initial starting point for modeling the efficiency performance of engineered systems. As illustrations, I present two examples, one from infrastructure management and one from transportation engineering.