I agree that BSL is the top contender for branching. It's definitely not as busy as the MFL with twice the tracks. If heavy rail is too cost-prohibitive, maybe light rail would work. Two tracks for the existing BSL and two for light rail branches, kind of like the MFL/subway-surface lines. Could even incorporate the city branch tunnel. Based on this random map I found (no idea how accurate it is) it seems like South Philly and NE Philly are the most under-served:
https://www.arcgis.com/home/webmap/viewer.html?webmap=db17469454894e159d882b1ed4b0aebf
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