Israel and Pakistan can't be allies for the same reason all conflicts in the world remain unsolved...when people believe in the status quo as the only real truth. For there to be progress, nations have to move past historic issues and into a more era-specific space of mind. The Israelis won't trust Pakistan because of our close relations to the Arab nations; while we'll avoid any official relations in the similar attempt to appease those very same Arabs.
In reality, we have gained nothing from our relations with the dictators of the middle east; instead allowing them to ideologically mold Pakistan into an extremist state. What better way to test out one's theories than to do so on a foreign people. We have turned into the guinea pig of the middle east. On the other hand, we may actually be able to learn greatly from the Israelis. Whether it is understanding how they have gained prosperity in the face of constant war or maybe, how they managed to maintain a strong military that is subservient, still, to the civilian government.
But allying ourselves with the Israelis is the surest way to anger the Arabs, who's charitable donations we have built our economic model around. So we are stuck in the status quo, as a resource starved nation in a hostile neighborhood; avoiding the one nation on this planet that maybe able to understand our current situation and in a position to help us move in the right direction...in favor of nations that have all the resources in the world and squandered them away.