Prior to Sunday’s announcement that Muslim-Brotherhood backed Mohamed Morsi had won Egypt’s presidential election, the Obama administration had expressed no public preference for the outcome. Whether the new government is run by Islamists or military-aligned autocrats, it holds little short-term promise for U.S. interests in the Middle East.

The inability to shape events in an important regional partner — the reluctance even to try, beyond exhorting Egyptians to “do the right thing” — would appear to leave the administration ripe for partisan criticism in a political season when President Obama’s “weakness” in the world has become a Republican mantra.

Meanwhile, GOP presidential candidate Mitt Romney has charged Obama with a lack of leadership on foreign policy issues from Syria to Iran to Russia to the European financial crisis, but neither Romney nor his surrogates have weighed in with a better idea on Egypt.

Even to Republicans, Egypt seems to exemplify the rule that there is only so much a U.S. president can do to run the world.

More than any of the Arab Spring countries, U.S. policy toward Egypt since its revolution began last year has been hemmed in on all sides. The secular democracy the administration once envisioned has not materialized because — as Secretary of State Hillary Rodham Clinton said ruefully last week — the youthful demonstrators who started the revolution “decided they wouldn’t really get involved in politics. ”

Attempts to organize them through aid to nongovernmental organizations backfired, leading to complaints of U.S. interference.

When the Muslim Brotherhood emerged as the only truly organized civilian force, the administration was faced with accepting an outcome that it had hoped to avoid. It has tried to swallow its concerns even as it has warned Islamists that Egypt’s precarious economy is not likely to survive the international isolation that extremism might provoke.

As an Islamic electoral victory appeared certain, Egypt’s generals threatened to renege on their promise to cede the power they have held since the fall of Hosni Mubarak.

In the past two weeks, the military has shut the doors of the newly elected parliament, written new constitutional powers for itself, and delayed revealing the outcome of the presidential vote. On Friday, after results of last weekend’s election were delayed, tens of thousands of Egyptians returned to Cairo’s Tahrir Square to warn of chaos to come.

The Obama administration defended the Egyptian military this year from a Democratic-led attempt in Congress to punish it with an aid cutoff. Now some U.S. lawmakers have renewed the push for punishment. But there is little indication that the generals are listening.

The Egyptian crisis, a former senior U.S. military official said, is a lesson on whether the era of buying relationships with powerful militaries abroad has outlived its usefulness. “What do we mean by a relationship? What are the pieces of it? In one sense, we gave them a lot of money,” he said. “That held us together.”

“But I don’t think we, strategically, put the pieces together for these countries in a way that makes a lot of sense,” the former official said, speaking of a series of administrations. “There’s a limited amount we can do. It’s not about their relationship with the outside world,” he said of the Egyptian military. “This is about the future of their people. However they get there, it’s up to them to decide.”

At risk is a bigger prize, at least from the U.S. point of view: the Egypt-Israel peace treaty. Both Congress and the Israelis think the military is “the best bet in preserving the peace treaty,” said Martin Indyk, who twice served as U.S. ambassador to Israel and now heads the Saban Center for Middle East Policy at the Brookings Institution. “The Israelis are saying don’t screw around with this.”

Indyk’s recently published book, “Bending History,” outlines the “inevitable tension between Obama’s soaring rhetoric and desire for fundamental change . . . and his instinct for governing pragmatically.” And he sees Egypt as offering a prime example. Beyond patience, some aid adjustments, and the administration’s near-constant warnings that America and the world are watching, “there isn’t a better idea out there,” he said. “What are we going to do?”

For the moment, there may be no other good options, said Stephen V. Hadley, who served as George W. Bush’s national security adviser and who has been floated as a possible secretary of state in a Romney administration.

“It’s a bit of a conceit that came out of the Vietnam era, that all would be right with the world if only the United States had the right policies,” Hadley said. “Well, I’m sorry. Would that we had that much control. But we don’t.”

Hadley has plenty of bones to pick with Obama on other issues. But revolutions like that in Egypt, which emerged from decades of dictatorship and suppression of dissent, “are long processes,” he said. “This is hard, what the Egyptians are trying to do. Let's give them a break.”

Hadley’s views are identical to those voiced by senior administration officials who spoke on condition of anonymity lest they be seen as trying to interfere.

“The reality is that these processes are, by definition, long-term, generational ones,” one official said. “You can’t measure it by six months, or even a year from now. It’s going to be going on for a long time.”