There are several reasons why applications in Islamabad might take a long time.
- it might be hard to staff the embassy there, since it is considered a dangerous place for Westerners
- Pakistan is violent, security checks might be difficult and extensive
- perhaps government documents are hard to verify, easy to forge
- perhaps Pakistan has acquired a reputation for marriage fraud
- perhaps Islamabad is also responsible for dealing with applications from Afghanistan, which might be even harder to process and clog up the system
I am sympathetic to both sides. This is a long process that destroys families and ruins opportunities; but Canada has to make certain that it is not importing violence. This country has a history of accepting sectarian troubles (Tamil, Sikh) and recently two terrorists killed in Algeria were Canadian citizens. There is no pressure in Canada to speed up immigration from Pakistan, and a lot of pressure to cut it off totally.
Remember, Canadian citizens do not have the right to bring their spouses here -- they have the right to apply. The Canadian government chooses the conditions under which they come. I am certain that this long wait is partly owing to Pakistan's violent society, which is no one individual's fault, but cannot be ignored by CIC.