Throughout the 18-days of the Egyptian protests, the Administration’s response was not always clear, ranging from support for Mubarak to a verbal nod toward the door.

Critics here say the unevenness of its public messaging deprived the Administration of an opportunity to exert more influence on the outcome through behind-the-scenes diplomacy.

“Anytime you have a situation like this, you’re going to have some confusion, no matter how well oiled the machine might be and how seasoned the people are,” William Cohen, Secretary of Defense under President Bill Clinton, told reporters. “Nothing is seamless. I think they corrected it as soon as they could.”

The most discussed story coming to the light is the major hiccup between Obama and Frank Wisner, Obama’s envoy to Cairo. Wisner told a Munich conference last week that Mubarak was indispensable to Egypt’s democratic transition, saying he “must stay in office” to oversee the changes he had ordered. [Clinton dumped National Security adviser Tom Donilon, originally scheduled to attend the Munich conference, at the eleventh hour for Wisner].

Obama was said to be furious, and it did not help that his Secretary of State, Hillary Clinton, Wisner’s key backer, appeared to be publicly siding with Wisner rather than the president, saying publicly that any credible transition would take time.

Clinton said the US backed “the transition process announced by the Egyptian government” — even as Obama was demanding that change in Egypt begin right away.

Obama was “seething about coverage that made it look as if the administration were protecting a dictator and ignoring the pleas of the youths of Cairo,” wrote the New York Times on Sunday, who then insisted that his renegades tow his line. “The president ‘made it clear that this was not the message we should be delivering,’” one official said.

It marked a low point in the administration’s response, said another official, who also requested anonymity.

Obama then told Vice President Joe Biden to take a hard line with his Egyptian counterpart, and told Senator John Kerry, head of the Senate Foreign Relations Committee, to counter the message from Clinton and Wisner when he appeared on a Sunday talk show.

Observers here say their trouble in sending a clear message was another example of how divided Obama’s team was, and divided on what to do.

The president first heeded the advice of the traditional foreign policy establishment led by Clinton, Biden and Defense Secretary Robert Gates, against that of a next-generation White House staff who worried that the American preoccupation with stability could put a historic president on the wrong side of history

Clinton and at State Department wanted to move cautiously, in part influenced by daily calls from Israel, Saudi Arabia and others who feared an Egypt without Mubarak would destabilize the entire region.

“There are different perspectives between the State Department and White House,” Michele Dunne, a former NSC and State Department official, among the Egypt experts invited by the NSC to offer counsel during the crisis, told reporters. While declining to comment on specifics, Dunne said the State Department and Pentagon were under pressure from allies such as Israel, Jordan and Saudi Arabia not to abandon Mubarak.

What became clear during the Egyptian revolt was the White House’s inability to influence events in the Mideast, which analysts and officials said became clear when Mubarak would not bow to US pressure to step down.

The US is no longer “respected, admired and feared” in the region as it was in the 1970s and 1980s, Aaron David Miller, former Mideast peace negotiator and State Department official now a fellow at the Woodrow Wilson International Center in Washington, told reporters. “We’re really marginal to this right now.”

Meanwhile, it didn’t take longer than a nanosecond for Republicans to pounce on the Administration’s handling of Egypt.

House Speaker John Boehner told reporters that the Obama administration had handled a difficult situation about as well as possible, but Republicans eyeing the presidency in 2012 used the Egyptian crisis to blast the White House.

Former Minnesota Governor Tim Pawlenty slammed the Obama administration’s response to protests in Egypt this Sunday on ABC’s This Week. He compared the White House response to the “Tower of Babel” and said the mixed messages added up to something “nearly incoherent.”

While former House speaker Newt Gingrich— while on a swing through Iowa, the state that holds the opening 2012 caucuses — said the president’s handling of the crisis had been “clumsy” and “amateurish.”

Gingrich said Obama’s administration has been sending confusing signals that could damage US credibility.

Meanwhile, Bruce Riedel, a former CIA officer who advised three US presidents on the Middle East and Central Asia, offered reporters sage advice about the current situation: “The genie is out of the box and the smart play now is to try to keep up with history, not hold it back, but not try to get too far in front of it either.”