Department of Defense Instruction (DoDI) 5000.02 does not include Systems of Systems (SoS) as a specific program type. Those are limited to Major Defense Acquisition Programs (MDAP) and Major Automated Information Systems (MAIS) Programs of various Acquisition Category (ACAT) levels. The SoS approach is alive and well, however, and is described in the Defense Acquisition Guidebook (DAG) and elsewhere as "a set or arrangement of systems that results when independent and useful systems are integrated into a larger system that delivers unique capabilities." Further, the DAG adds that "nearly all DoD systems function as part of an SoS to deliver a necessary capability to the warfighter" and that "SoS systems engineering (SE) is an ongoing iterative process".
The DAG and SE documents referenced above all advise that when formulating an acquisition strategy for a SoS effort, it is important to coordinate and balance the requirements of constituent systems. A best practice discussed in the DAG is to establish a senior governance body as a forum for discussion and decisions related to functional capabilities, technical plans, configuration management and strategies with respect to interfaces, interdependences, risks and risk mitigation. It is critical to address all equities and make collective decisions that can be implemented in changes to a system’s configuration.
Another SoS best practice is to monitor closely interdependent programs, with checkpoints at scheduled design reviews to assess program progress, assess related risks and determine actions to mitigate potentially negative impacts. Another best practice is to have the technical representatives from each system participate in each others’ System Functional Review (SFR), Preliminary Design Review (PDR) and Critical Design Review (CDR).
For a more detailed discussion of SE for SoS - including linkages to acquisition and sustainment processes and challenges, recommend accessing the following report:
The Office of the Deputy Assistant Secretary of Defense (ODASD)SE has the following webpage dedicated to the topic of SoS SE: https://www.acq.osd.mil/se/initiatives/init_sos-se.html. It includes linkages to the DoD SE Guide for SoS, for one thing (https://www.acq.osd.mil/se/docs/SE-Guide-for-SoS.pdf), plus other useful information and links.