Geography is manifest destiny... PR will never be able to compete with CX/SQ/TG/EK on Kangaroo route, and it will never be able to compete with KE/OZ/JL/NH on North America transit to China. And unlike CI/BR, it doesn't have a robust enough O&D premium business traveler market to sustain long haul service or massive short haul traffic to China/HK to pay the bills.
I don't really have a solution to offer but PR is an classic case where Govt subsidy is probably inevitable if it is important for the country to have its own long haul carrier. There is a reason why the Scandinavian countries pooled their resources and formed a multi-national flag carrier. They couldn't compete with better situated flag carriers based in London, Paris, Amsterdam, or Frankfurt. Sometimes, there is no overcoming geography.