Mossad is an exceptionally well-run organization.
They have been active in Pakistan for decades --- most notably during the Afghan War and our nuclear program. In addition to SIGINT/ELINT, Mossad had a few highly experienced agents in-country collecting HUMINT on AQ Khan. They disguised themselves as fishermen on Rawal Lake; their fishing rods had sophisticated long-range mics in them and they recorded conversations AQ Khan was having with 2-3 colleagues about his plans. This was passed on to the CIA and various assassination plans were prepared.
Since then, they have been active in running various agents and moles in a number of departments. Their prime target has remained our nuclear program and they have achieved some success in keeping tabs/infiltrating it. India and Israel have been cooperating increasingly on the security front and it's an open secret that Ajit Doval feels the Mossad model of aggressive covert action is the best way forward for Indian external intelligence and he actively fantasies about RAW reaching that level of expertise.
Given our pathetic governance, lack of merit in almost all government instituitions and a hopelessly corrupt and courage-less leadership, we are exceptionally vulnerable. Many Israeli leaders, on the other hand, have served in tough defence-related postings and are pretty hawkish about national security. This conceptual and intellectual difference cannot be overstated enough. This is Pakistan's biggest weakness.
Mossad, unlike the ISI, does not need to worry about internal security (the Shabak --- AKA Shinbet --- takes care of that; totally different organization with its own recruiting, hierarchy, techniques, etc.).
They benefit from dedicated organizations for biowarfare (increasing a country's disease stress + coming up with untraceable toxins for assassinations; accusations include testing new poisons on Palestinian prisoners), cyber warfare (hacking, eavesdropping; one of the best in the world since they recruit their CS/IT students and "graduates" of the Unit 8200 have gone on to found/lead various successful tech start ups), etc.
Within Mossad is the "holy of holies" --- the Kidon Unit, solely responsible for external assassination. They are HQ'd separately and don't reveal their real identities to "regular" Mossad officers, including seniors during briefings. Imagine a unit that spends all of its time coming up with innovative ways to kill those deemed significant threats to Israel's interests. Many of these are pre-emptive (like the assassination of a Syrian Brig General in his beachfront villa a few years ago and the killing of a Canadian long-range gun designer who was developing a weapon for Saddam).
Finally, Mossad selection and training is amongst the toughest in the world. Training time before qualifying to become an officer is significantly more than the ISI and all officers, with the exception of the Director, are recruited and trained under the same rigorous guidelines --- unlike the ISI, where many (not all) officers are simply posted from their military units before "rotating out" again.
So, combining significant financial and intellectual resources results in a ruthless organization that is small, nimble and innovative. The ISI's Counter Intelligence Wing needs to seriously step up its game; and our S Wing should closely explore case studies of Mossad's external exploits to build additional capacities of its own.
Happy to answer questions if you guys have any.