Getting around Pakistan may be done in any of several ways, although it should be mentioned from the very start that getting around Pakistan by boat is not a popular or smart option, despite the presence of some significant river tributaries in the country and its coast. The water-based domestic transport of Pakistan is not very well developed, and even entry into the country is not typically done over the sea. As such, most people going about Pakistan do so overland or-in special cases-by air.
It would be easier to take the special case first: getting around Pakistan by plane is generally only done by those headed to the north in search of mountain-climbing opportunities around places like Gilgit and Skardu. This would certainly be the easier option compared to travelling to them over land. The only problem is that there are relatively few flights when compared to the number of persons actually seeking to go to those areas, which means you may well have to book your ticket in advance to guarantee yourself a seat. Furthermore, you need to check the travel advisories for the weather in the area, because sudden cancellations are not unheard of.
Most of the transport in Pakistan is on land, though, and this is actually reflected in the state of its roads: it has a remarkable number of roads, especially in the cities and between them, and its highways are generally in better condition than those of its neighbours, India included. Hence, most people prefer the landlubber’s options when in the country, choosing to look into ways of getting around Pakistan on land.
Car rentals are possible in the country but not advisable, given the choked state of the city streets (it would be a different situation if you plan to go to less densely populated and more rural locations, of course). There are a lot of cars in the country, and driving here could easily rob any tourist of his enjoyment during sightseeing. It would be far easier to take the buses, cabs, or autorickshaws for local transit.
Buses are ubiquitous and generally lack air-conditioning, although there are a few luxury ones catering to those willing to pay a higher fare. They are fairly reliable if you want to get somewhere quickly, although taller persons may find many of the seats (especially those in the old minibuses) to be rather cramped for space. As for the cabs, you may negotiate with them for a price or demand that they use the meter: it is dependent on you which method is preferable, although it is best to have a local with you either way to ensure that you do not get tricked into paying more than you should. And the autorickshaws are just like those you would find in India: plentiful, cheap, fast, and a bit dangerous on the whole. Note that there are even places where you shall be able to find an old form of transport right next to modern cars: a donkey-drawn cart ambling down the asphalt road.
The last option for those getting around Pakistan overland is the train… although it is no longer as popular as it used to be. There have been major changes and alterations in the railway system that have resulted in reports of trains not being on time and fewer trains being operated. Most transport has shifted to the roads, so your chances of getting where you want to go quickly might be better were you to look into highway transport options instead.