A holistic approach to decision-making in energy systems is vital due to the complexity and interconnectedness of modern energy systems. This approach considers various factors such as economic viability, technological feasibility, environmental impact, and social acceptance. By integrating these diverse elements, decision makers can identify more economically-feasible, sustainable, and resilient energy strategies. However, decision makers often rely on a narrowly-focused approaches such as economic assessments for energy system strategy selection. While these focused approaches are valuable since they provide clear metrics of potential solutions, e.g., economic measure of profitability, they do not offer the much needed system-as-a-whole understanding which often leads to the selection of sub-optimal or not feasible solution, the fact discover much later in the process when the change may not be possible. This paper reviews the current approaches to decision making in strategic planning of energy systems and concludes that the existing approaches have gaps and challenges. This paper presents a novel evaluation framework to support holistic decision making in energy systems. The framework is based on systems thinking approach, applied through systems engineering principles and tools, coupled with a multicriteria decision analysis approach. The systems engineering approach is guiding the process of the development of feasible solutions for a novel energy systems and the multicriteria decision analysis is used for a systematic evaluation of available strategies and objective selection of the best solution. The proposed framework enables a holistic, multi-disciplinary, and objective evaluations of solutions and strategies for energy systems, clearly demonstrates pros and cons of available options, and supports knowledge collection and retention to be used for a different scenario or context. The framework is demonstrated in a case study evaluation solutions for a novel energy system of clean hydrogen generation.