This dissertation presents a set of analytical tools developed to investigate the energy system transition using a systems approach. The cases explored range from Kosovo, a country on the verge of new electricity supply investments, and future energy pathways to an analytical investigation of innovation in battery storage systems that could unlock the environmental and health benefits of intermittent renewable energy sources such as solar and wind technologies. The analytical tools compare existing metrics such as levelized cost of electricity with new metrics such as a two-factor learning curve of deployment and innovation and trace metal content of coal per final kWh of electricity delivered and energy return on investment of distributed energy systems.Chapter 1 investigates the case of Kosovo and introduces an analytic framework to analyze electricity costs and environmental impacts of future electricity options. The scheduled decommissioning of the Kosovo A coal-fired power plant provides an opportunity to investigate the changing cost of alternative energy options available in Kosovo for new energy infrastructure. I find that a range of investment pathways from international financial institutions and donor groups could meet the same projected electricity demand at a lower cost than building a new 600 MW coal fired power plant. The options include energy efficiency measures, combinations of solar PV, wind, hydropower, biomass, and the introduction of natural gas. The results indicate that financing a new coal plant is the most expensive pathway to meet future electricity demand in Kosovo.Chapter 2 utilizes the analytic framework developed to estimate the cost of future electricity pathways and uses green chemistry and public health risk assessment to estimate trace metal content of coal and investigate the air-pollution-related-health risks of lignite coal in Kosovo. By utilizing ICP-MS, I sample lignite coal for trace metal content and develop a risk model to