I followed some Twitter troll fight during their flooding crisis. Apparently they have some constitutional amendment which gives local/state governments complete ownership of their local issues.
I don't recall what that was. But it looked like classic central government vs state government fight.
If I were to guess, it is because the political power has long rested with Pakistani Punjabis and Lahore is their capital city. Whilst Karachi has long been relegated as city of migrants.