After U.S. Secretary of Defense Robert Gates' visit to Pakistan aimed to strengthen relations with a key regional ally in the fight against militancy, a number of challenges still remain. Not least of all is the lack of trust between the two nations.

There are "deep problems plaguing the bilateral relationship such as the ongoing trust deficit," said Malou Innocent, foreign policy analyst at the CATO Institute.

While leaders of the two countries have stated their desire for a long-term partnership, Pakistan views the United States as a fair-weather friend interested solely in short-term strategic gains.

Pakistani Prime Minister Yousuf Raza Gilani was quoted on Thursday by Pakistan's Daily Times newspaper as criticizing the "discriminatory U.S. attitude" toward Pakistan.

For their part, U.S. officials have questioned Islamabad's commitment to fighting terror groups and accused its military of taking on only those terrorists who target Pakistan, not those plotting against India and the United States.

Pakistan counters that it cannot fight all militants simultaneously.

Analysts said the move was a snub to the United States, as Washington wants Pakistan to extend its military efforts to cross-border attacks in Afghanistan.

Al-Qaida leaders are believed to be hiding out in ungoverned tribal areas along the Pakistan-Afghanistan border since the U.S. invasion of Afghanistan in 2001.

"The Pakistanis haven't provided a warm reception to Gates in that they made clear that Pakistan wasn't anxious to start an offensive in North Waziristan anytime this year," said Lisa Curtis, a fellow at the Heritage Foundation. "So this visit doesn't seem particularly successful in closing gaps."

Gilani reiterated his government's disappointment with the ongoing U.S. drone strikes along the border with Afghanistan, saying the attacks hampered efforts to separate militants from the local population.

"One stumbling block with continued airstrikes is that they fuel Pakistan's indigenous Taliban insurgency," Innocent explained.

While unmanned aerial vehicle (UAV) attacks target terrorists, hundreds of bystanders have died in the crossfire, which has stirred anti-U.S. sentiment among many Pakistanis.

"This is our war, and drone attacks are having serious implications (for the war against extremism). They should be avoided," the Daily Times quoted Gilani as saying.

Still, some analysts said there is an unwritten agreement that a certain amount of UAV strikes are tolerable.

"There are innocents killed, but the people in the area don't get up in arms," said Kamran Bokhari, regional director of Middle East and South Asia Analysis at Stratfor, a global intelligence company.

He added that many in the area want to be rid of the Taliban. "They don't applaud (drone attacks) but will tolerate them."

A plan is now underway for the United States to give unarmed drones to Pakistan. That could make the government of Pakistan appear stronger in the face of militants, Innocent said.

It will also allow Pakistan to have more say over who drones targets, she added.

Despite his criticism, Gilani said he wants a long-term relationship between the two countries and that the "trust deficit" could be lessened by improving perceptions and promoting more contacts between Pakistani and American citizens.

He added that the fight against militancy was a long-term struggle that required ongoing improvements to security forces.

In an op-ed published Thursday in The News International, Pakistan's largest English-language newspaper, Gates pressed Pakistan to target Afghanistan's Taliban leaders, the Quetta Shura, who are holed up in Pakistan's Baluchistan Province, located outside of tribal areas.

"Maintaining a distinction between some violent extremist groups and others is counterproductive," he wrote. "Only by pressuring all of these groups on both sides of the border will Afghanistan and Pakistan be able to rid themselves of this scourge for good."

Still, he applauded the Pakistani Army for its anti-terror operations in the Swat Valley and South Waziristan, noting that Pakistan's army saw nearly 2,000 casualties over the last three years.

Gates said his key message for the visit was that the United States is committed to a long-term relationship with Pakistan. Washington has learned from past mistakes and will not abandon Pakistan in the future, he said.

"The main focus of my visit is to provide reassurances that we are in this for the long haul and intend to continue to be a partner of theirs for far into the future," he said.

Washington seeks to bridge the gap with Pakistani military leaders and end the lack of trust that has put a damper on cooperation against extremism, Gates said in a speech Friday to army officers at Islamabad's National Defense University, Pakistan's most prestigious military academy.

Analysts said that despite the hurdles, more than a dozen in-person meetings between Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff, and Pakistani Gen. Ashfaq Kayani have undoubtedly helped promote the relations between the two nations.