Egypt's new second-in-command of the military has said that U.S. troops should be withdrawn from the Middle East while any democratisation in the region should come from within and have religious legitimacy, according to a paper he wrote in 2005.

Though published before U.S. President Barack Obama was elected, the document written while newly appointed Chief of Staff Sedki Sobhy was studying in the United States offers a rare insight into the thinking of a top officer in the traditionally opaque Egyptian army.

The generals, who for decades stayed in the shadows, were thrust to the fore when Hosni Mubarak, himself a former air force commander, was toppled in an uprising last year and the Supreme Council of the Armed Forces took charge.

An Islamist president, Mohamed Morsi, came to office in June and stamped his authority over the military this week by retiring the country's two top generals and taking back vital powers they had earlier retained for themselves.

Though generals held news conference and gave interviews when in charge, they gave little away in public about their thoughts on broader policy beyond the transition, such as the crucial relationship with the United States, which gives Egypt $1.3 billion in military aid a year and trains many officers.

"I recommend that the permanent withdrawal of the United States military forces from the Middle East and the Gulf should be a goal of the U.S. strategy in this region," wrote Sobhy, then a brigadier general studying for a Master of Strategic Studies Degree at the U.S. War College.

He added in his concluding remarks to the 10,600-word thesis "that the United States should pursue its strategic goals in the region through socioeconomic means and the impartial application of international law", in a reference to what he had earlier described as Washington's "one-sided" relationship with Israel.

He said the presence of U.S. troops in the region had been used as a justification for armed struggle by radical Islamists.

Though many in the Middle East object to U.S. soldiers being posted there, it is unusual to hear the view aired so clearly by a senior figure in the army of Egypt, a staunch U.S. ally.

Sobhi, 56, was appointed chief of staff, the military's second most senior post, in the surprise shake-up announced on Sunday by Morsi, whose Muslim Brotherhood group was routinely hounded and jailed in the past six decades by Mubarak and other presidents who all hailed from the military.

COMMUNICATION

The army's top officer, Field Marshal Hussein Tantawi, who served as Mubarak's defence minister for 20 years and led the military council, was forced into retirement, replaced by General Abdel-Fattah el-Sisi, the former head of intelligence.

Sobhi said there was "a fundamental lack of understanding and communication" between foreign policy makers from U.S. administrations and governments in the region, writing before Obama sought to shift U.S. policy by reaching out to the Arab and Muslim world with a pivotal speech in Cairo in 2009.

The general said one reason was U.S. policy makers worked in a strictly secular democratic system but: "The Islamic religion is strongly interlinked to various degrees with the functioning of most Arab governments and their respective societies."

The process of democratisation "must have and project political, social, cultural, and religious legitimacy. In other words, this democratisation process must be of and viewed as having a purely domestic origin," he wrote, highlighting in italics the words "religious", "viewed" and "purely domestic".

He said Washington should turn its focus to a "new Marshall Plan", mirroring the huge package of aid that helped Europe rebuild after World War Two, to regain its influence.

Sobhy's thesis was posted on a U.S. Department of Defense website, and was initially highlighted by blogger and analyst Issandr El Amrani.

The dramatic army changes followed a military blunder on Aug. 5 on the Sinai border with Israel when 16 border guards were killed by militants, giving Morsi an opening to act amid public anger and - some more junior officers said - grumbles among some military ranks over the army leadership.

RELIGIOUS ALLEGIANCE?

The generals have shown no sign of challenging Morsi's decision. Tantawi and former Chief of Staff Sami Anan were both warmly greeted and awarded medals by the president in a ceremony shown on state television on Tuesday.

One Western diplomat and other observers have suggested the new commanders may have Islamist sympathies or hold conservative values that may appeal to the Brotherhood. But others played down such talk, including Robert Springborg, a professor at the U.S. Naval Postgraduate School in California.

Writing in Foreign Policy, he said the main reason for removing Tantawi "was not Islamist commitment, but accumulated dissatisfaction with the field marshal's debasement of their institution and its capacities, triggered by his inept political manoeuvring".

The Western diplomat said some discontent may have prompted the change, including from U.S.-trained officers imbued with the idea that the army should stay outside politics.

Sisi's intelligence background, suggesting a deep knowledge of army personnel, could have made him an attractive ally for Morsi, the diplomat said. "He is the best person to have on your side. You promoted him, you own him," he said.

Washington has urged the new commanders and the civilian authorities to work together on Egypt's democratic transition.

"These new appointees, the new leaders of the military are all people that we have worked with before and many of whom have trained here in the United States as well," said U.S. State Department spokeswoman Victoria Nuland.

Among the other promotions was General Mohamed el-Assar who was appointed deputy defence minister. He has been in charge of relations with the United States, one reason that may have helped his promotion as well as the fact that he spoke out early after Mubarak's ousting against the former president.

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