I believe we are going in the right direction but eventually we would need to separate legislature and executive and devolve of their powers, given the diverse nature of our country. The structures might look something like:
Legislature:
More or less similar structure but dividing existing lower house constituencies further and have ~400 seats. There is no point in having reserved seats for females and minorities if they cannot vote against party lines in the assembly.
Senators (equal representation from all provinces) should be directly elected by the people and not through lower house. There is no point having a senate if it is a reflection of national assembly. Senate should be the primary policy making body for sensitive and important issues, specially for fiscal, external relations and inter-provincial matters.
Executive:
The structure could look like this:
Councilors → Mayors → Governors —> President.
Ideally, we need to have ~15 provinces with Governors as executive head of each. Mayors should have some law making authority (specially revenue, development, health, transport and education related laws) in addition to executive powers. Authorities like police and FIA should be reporting to the elected executives (Mayors and Governors). Major cities should be run as independently as possible, through mayors and councilors.
All of these should be directly elected by the people and not appointed.