System integration is one of the key challenges to bringing future hybrid-electric and all-electric aircraft into the market. In addition, retrofitting and redesigning existing aircraft are potential paths toward achieving hybrid and all-electric flight, which are even more challenging goals from a system integration perspective. Therefore, integration tools that bridge the gap between the aircraft and the subsystem level need to be developed for use in the conceptual design stage to address current system integration challenges, such as the use of space, the share between propulsive and secondary power, required level of electrification, safety, and thermal management. This paper presents a multidisciplinary design analysis (MDA) framework that integrates aircraft and subsystem sizing tools. In addition, this paper includes improved physics-based subsystem sizing methods that are also applicable to smaller, commuter, or regional aircraft. The capabilities of the developed framework and tools are presented for a case study covering the redesign of the DO-228 with a hybrid-electric propulsion system in combination with the electrification of its systems architecture and different subsystem technologies.