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Why has it become so hard for them to prevent regular and frequent bombings on civilians by domestic and foreign terrorists given that they allegedly have one of the best intelligence agencies in the world?
Israel has been able to get rid of this nuisance very effectively. So why can't Pakistan?
What factors are making the process complicated?
There are many reasons:
Pakistan has 189 million people while Israel has 8 million people (including, for example, the West Bank and Gaza Strip) (about 22 times as large).
Pakistan has 307,374 square miles of territory while Israel has 8,019 square miles of territory (for the same definition of Israel) (almost 38 times as large).
Pakistan's "tribal areas" which are the source of many bombings like the West Bank and Gaza Strip in Israel which is home to many bombers when this was a common occurrence in Israel, are both only weakly under the control of the central national government's authority, but it is much more practicable for Israel to wall off the areas that it does not fully control (which was the single most important policy decision that led to fewer bombings in Israel) than it is to do so in Pakistan. Further, while almost all bombings in Israel had ties to territory that it did not fully control, a significant share of the bombings in Pakistan have origins in its main, more fully controlled territory.
The political factions in Israel (including the West Bank and Gaza Strip) that supported bombings in Israel had absolutely no representation of even remote allies in the national parliament in Israel, while the political factions in Pakistan that support bombings in Pakistan have some significant political allies in the national parliament.
There are news reports (some of which are leaked from U.S. intelligence sources) that some parts of the Pakistani government bureaucracy is not concerned about the bombings, while other parts of the Pakistani government very much wants to end them (see, for example, here). In general, there is a divide between the military and civilian parts of Pakistan's government and this divide plays an important role in its politics (which is also true of many other countries that are relatively newly democratic such as Turkey and Egypt).
There is a deep ethnic divide between the political factions in Israel that backed bombings and the populations in Israel that were the target of the bombings, with almost no overlap, that is very easily discerned with superficial examination. In Pakistan, in contrast, bombings are driven by religious differences between people who are ethnically much more similar within a multi-ethnic panorama of predominantly Muslim ethnicities - indeed, often the targets of bombings are secular people, or Christians, or less "fundamentalist" Muslims of the same ethnicity as the bombers, so simple ethnic profiling is not very useful in making a first order assessment of the risk that someone is a bomber and generates vastly more false positives. It is much easier for a bomber to "pass" as a member of a target population in Pakistan than in Israel.
In part because the bombings in Pakistan are not targeted at an ethnic group per se, they are not viewed as an existential threat in the same way that they were in Israel, so there is a less urgent need to stop them.
Pakistan's government is more corrupt and less effective generally than Israel's government. More generally, Pakistan's government has less control over even the territory that it has more control over formally, than Israel does over the area it has more control over formally. This is typical for almost all economically developing v. economically developed countries relative to each other. Preventing bombings requires more social control and lots of economic resources.
Israel is a heavily militarized society with a percentage of people in military service to some degree unmatched almost anywhere else in the world but North Korea, Pakistan is not.
Stopping terrorist bombings is very hard. Many countries (e.g. Russia, France, Germany, the U.K., Spain, the United States, Iran, India, Nigeria, Kenya) have been unable to stop them. Israel's progress in this regard is the rare exception rather than the rule.
