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President-elect Barack Obama impressed scholars, historians and even Republicans as he quickly filled up his Cabinet and made top appointments with little drama in the weeks following his election.

But the once wrinkle-free transition has hit distracting snags with Inauguration Day just two weeks away. And Republicans and Democrats alike are grumbling about the president-elect's latest decisions.

The bumps in the road come at an inopportune time. Obama has tried to use his political capital to shore up support for a massive economic stimulus program; instead, he is dealing with questions about missteps in assembling his administration-to-be.

Obama, for instance, had to apologize to Democratic Sen. Dianne Feinstein on Tuesday for failing to consult her on his decision to name former Bill Clinton chief of staff Leon Panetta as CIA director. Feinstein is the incoming chairwoman of the Senate intelligence committee.

"It distracts from the larger agenda of the president-elect," said David Lewis, a Vanderbilt University professor who works with the White House Transition Project, a resource of experts for transition teams. "He jeopardized his ability to push through this (economic recovery) legislation early on."

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Three developments over the past week have tripped up the Obama transition. His pick for commerce secretary, New Mexico Gov. Bill Richardson, withdrew his nomination Sunday, citing concerns that a federal probe involving his administration might take longer than anticipated. On Monday, news broke that Panetta is Obama's choice for CIA chief -- even though he has little experience in intelligence circles and Obama did not consult key lawmakers on the decision.

And Roland Burris, a former Illinois attorney general, was appointed last week to Obama's Senate seat by Illinois Gov. Rod Blagojevich, even though the governor is facing charges for trying to sell that seat. Obama and his aides had tried to keep a safe distance from the investigation, but Obama jumped into the fray by siding with Democratic leaders in declaring that Burris should not be seated.

Democrats now face the possibility of a lawsuit after denying Burris entry to the Senate Tuesday, as Burris' attorneys claim the Senate has no legal ground to reject him.

Republican strategist Terry Holt said these hiccups have been mostly "self-inflicted," despite Obama's promising start.

"He's been both brilliant and clumsy all in the space of a very short period of time," Holt said.

Holt said Obama and Senate Majority Leader Harry Reid painted themselves into a corner by refusing to consider Burris. He said they ironically ensured that Burris would receive more attention in the media, and suggested the two Democrats retrace their steps to allow Burris entry.

"He's burning up an awful lot of goodwill on things that aren't, in the end, very important," Holt said of Obama.

Obama seems to be trying to restore some goodwill when it comes to his selection of Panetta for CIA chief.

On Monday, key members of the Senate intelligence committee, including Feinstein, D-Calif., complained that they were not consulted on the selection. "I know nothing about this," Feinstein said in a written statement, and she suggested Panetta would not be her choice, stating she wants an "intelligence professional" in that role.

"Probably they could have done a better job" floating Panetta to senators, said Lanny Davis, former White House counsel to Clinton.

"There was a snafu in the failure to notify Senator Feinstein and Senator (Jay) Rockefeller," Sen. Evan Bayh, D-Ind., said. "That should have happened."

But Bayh and Davis both defended Panetta's credentials. Some in Washington are inclined to accept an intelligence outsider in the CIA, suggesting Obama erred more in the execution than the actual selection.

Obama on Tuesday personally apologized to Feinstein. And Vice President-elect Joe Biden told reporters that the lack of communication was "just a mistake."

Other Democrats, including Wisconsin Sen. Russ Feingold and Texas Rep. Silvestre Reyes, came out in favor of Panetta on Tuesday.

Lewis said Obama needs to continue to smooth the ruffled feathers and line up Democrats in support of Panetta, to prevent the appointment from becoming a distraction down the road.

Obama, while not confirming Panetta as his choice, told reporters Tuesday that he has the "utmost respect" for him and that Panetta was "fully versed" in international affairs as former White House chief of staff. He said he would put together a "top notch intelligence team."

The transition speed bumps come as a surprise, since Obama seemed to have wrapped up the bulk of his key staffing decisions more than two weeks ago, with a month to spare until Inauguration Day. Many of his selections were heralded as moderate, experienced choices with a very good chance of clearing the Senate confirmation process.

But although Panetta could prove divisive, Obama also has to deal with the opening created by Richardson's withdrawal over the weekend. The New Mexico governor cited his concern that a federal probe into possible "pay-to-play" schemes would drag out through the confirmation process.

Many wondered how Obama's team could miss such an apparent problem with Richardson's application.

"Their vetting process was supposed to have been so great," said Lonna Rae Atkeson, professor of political science at the University of New Mexico. But she noted that reports about the Richardson investigation had been in the local media long before he was put up for commerce secretary.

She questioned why Obama would drop Richardson so readily if he knew about the investigation from the start.

Lewis said Obama has to take extra care in finding a problem-free replacement for the New Mexico governor.

"You don't want to have problems arise two times in a row on the same position," he said.

There have already been mixed messages coming out about the opening created by Richardson's departure.

Despite chatter late Monday in Washington state that Gov. Christine Gregoire would be named to the post, aides to Obama told FOX News that she is definitely not going to be Richardson's replacement. They said "others" are pushing Gregoire for the job.

It's unclear who Obama is considering or when he'll announce a nominee.

FOX News' Judson Berger, Jim Angle and Major Garrett contributed to this report.