The biggest problem with a Karachi registered car is renewal of registration. It has to be done in Karachi, which is a headache for people with no links or connections in Karachi. The next is rust. A car in Karachi deteriorates much faster in Karachi than in Lahore or Rawalpindi. Third is high mileage. Most cars in Karachi run up mileage as distances within the city are quite large.
In my opinion, cars in Karachi are generally cheaper as Karachi people are mostly from the business community who have the resources to change cars frequently. So after every 3-5 years people replace cars thereby keeping the used car market large. In Lahore or Rawalpindi, once a car is bought it remains in the family for at east 10 years or more.
Just be careful if buying a car in Karachi. Original embossed number plate with Sindh seal mark. Original papers with verified file. CPLC verification. Maybe a few other checks also. Good luck.