Would strongly advise against purchasing a Picanto, selling it is a pain.
You could easily purchase the new Yaris Hatchback in the same price with much better fuel average, comfort, reliability and resale but of course it is up to you at the end of the day as the Picanto is decent despite perhaps not better than the competition.
As for your questions, I own a Sportage so I can answer some of them:
1) KIA Macca & Clifton are known to be very decent but of course experiences can vary person to person.
2) Yes you can, but may cause issues with the warranty if the branch you bought from are in the mood to cause issues.
3) It is an econobox car, you should not look to upgrade Wheels / Tyres as they are completely fine, why spend the extra money when the comfort of the car is not going to be great to begin with. But if you wish to you of course could opt for Yoko's for less noise and more softness. The Tyres that come with the car are EURO Tycoons which become hard after 5-10k KM's but easily last till 40k KM's or 5 years.
4) Get your car detailed on the exterior, you should wax it monthly and avoid dusting or washing the car dry as that induces swirls and scratches into the paint. When washing either wash using water, car shampoo and proper towels for drying or use a waterless wash chemical and multiple microfibers to keep the paint in good condition. You may also choose to ceramic coat the car if you wish to avoid waxing monthly.
5) PPF'ing a econobox car makes no sense. A good PPF will set you back at least 2 lac, anything under that is definitely not a PPF, just plain old fraud. That is almost 5% of the value of the car, makes no sense to do so. Better to just repaint a panel that is damaged if and when needed.
6) Registration, Insurance and Tracker are a must in Karachi. Should not take more than a week for all three.
7) Adamjee is generally the best and process claims the easiest.
8) Use good quality filters and Oil. Drive Carefully and in Good Health!