At least the railway lines, and their right of way, are saddled with old property disputes, and there could be issues with convenience.
There is no excuse for not creating separate cycle and two wheeler pathways on flyovers, and, especially, bridges over the sea, rivers and creeks (this is specific to Mumbai, mainly), where the additional load bearing factors would be minimal, but the payback, in terms of service delivery for millions of commuters, would be extensive.