Indonesia's archipelagic geography presents unique challenges for the energy transition in isolated microgrids, where 598 installations with capacities below 1 MW predominantly operate on diesel generators, incurring significant economic and environmental costs and totaling 12 million tons of carbon emissions annually. However, existing studies predominantly address single-site hybrid renewable energy systems and do not provide a systematic, multi-location framework that links site-specific resource conditions to optimal system types (OST) and explicit energy transition pathways. This study presents a comprehensive optimal system type framework for techno-economic optimization of hybrid renewable energy systems across 130 isolated microgrid sites in Indonesia. The methodology integrates load profile clustering, renewable resource mapping, and sensitivity analysis to determine optimal configurations encompassing photovoltaic panels, wind turbines, diesel generators, battery storage, and power converters using HOMER Pro software. Load clustering analysis produced six distinct groups with strong validation metrics. At the same time, a validated generic model achieved exceptional accuracy, with a coefficient of determination of 0.985 and a Mean Absolute Percentage Error of 2.01 percent in the multi-location analysis. Case studies at four pilot sites demonstrated average Net Present Cost savings of 37.2 percent, Levelized Cost of Energy reductions of 37.1 percent, Return on Investment of 10.4 percent, and Renewable Fraction of 81.0 percent compared to diesel-only baseline systems. Beyond conventional techno-economic assessments, the proposed framework introduces a quantitative threshold analysis that identifies resource and fuel-price tipping points for technology transitions and synthesizes these findings into a multi-phase energy transition roadmap tailored to Indonesia’s national de-dieselization program. Threshold analysis identified critical transition points at a wind speed of 2.95 meters per second and Global Horizontal Irradiance levels of 5.2 and 5.5 kilowatt-hours per square meter per day for optimal technology selection. Under high-fuel-price scenarios of 1 US dollar per liter, 70.8 percent of locations achieved complete diesel elimination with pure renewable systems combining photovoltaics, wind turbines, and battery storage, while 29.2 percent retained hybrid configurations. The framework provides strategic guidance for Indonesia's national de-dieselization program targeting 5,200 diesel generator units across 2,130 locations, supporting Enhanced Nationally Determined Contribution targets and net-zero emissions by 2060. © 2025, School of Electrical Engineering and Informatics. All rights reserved.