President Obama and Senate Majority Leader Harry Reid (D-Nev.) (Evan Vucci/AP)

President Obama, Senate Majority Leader Harry M. Reid and other Democrats have made a concerted effort over the past two years to seat as many federal judges as possible, and they could declare victory, having confirmed the most judges in a single Congress since 1980. But this strategy — based on the political calculus that lifetime judicial appointments will have greater, longer impact than executive-branch nominees — means some federal agencies will still face serious gaps during Obama’s remaining time in office.

In private conversation with a Republican senator earlier this year, Reid (D-Nev.) acknowledged that confirming federal judges was his “top priority,” according to an aide to the GOP senator, because “it’s what lasts.”

While Senate Democrats were able to confirm dozens of the president’s stalled nominees in the final legislative frenzy before Congress adjourned for the year, the Obama administration will enter its last two years with more than a quarter of its senior Cabinet agency posts — 96 presidentially appointed positions — unfilled, according to a White House analysis. The reason, in most cases, is that nominees for those jobs have not been confirmed by the Senate.

But which nominations advance to confirmation and which ones flounder has become a political choice that reflects the ideological divisions that now define Washington.

Reid spokesman Adam Jentleson said that given the fact that federal judges serve well beyond the course of a single administration, “one is truly a legacy situation and one is less sweeping.” But he added that Reid had tried, under difficult circumstances, to confirm key agency nominees where it made a difference.

Congress has approved a smaller percentage of Obama's White House nominees than either Clinton or Bush.

“It was a triage situation, and we tried to address the crisis where it was the most acute,” he said, noting that while Reid has had more latitude in calling up nominees, he has been limited by time available to debate the nominations.

The feud between Democrats and Republicans on the issue reached a low point in November 2013, when Democrats were so frustrated with their efforts to seat three judges on the U.S. Court of Appeals for the District of Columbia Circuit, they lowered the threshold for confirmations by eliminating filibusters for most of the president’s nominees.

Sen. Lamar Alexander (R-Tenn.), who has helped broker bipartisan deals on the confirmation process in the past, said in an interview that by upending the rules, Democrats have undermined their ability to seat future nominees in the GOP-controlled Senate.

There was a price to pay. Alexander noted that there are more nominees that have cleared committee and are waiting for a vote than on Nov. 21, 2013, when Senate Democrats changed the confirmation rules.

Most lawmakers and academic experts said it will be increasingly difficult for Obama to win approval of his executive-branch nominees during his last two years in office.

“He’s created an environment where in the new Congress, it’s going to require a huge attitude adjustment to get anyone confirmed,” Alexander said of the president. “They’re not going to be able to send us anyone they want to. Those people will never see the light of day.”

A bipartisan resolution that dramatically cut down the floor time for most nominees will expire at the end of this Congress, meaning every nominee will be subject to 30 hours of debate. And some nominees have begun to give up on the process out of frustration.

White House press secretary Josh Earnest said Tuesday that he expected some Republican senators “will attempt to capitalize on their new majority to prevent the president from appointing highly qualified individuals to serve the American people,” but this strategy could backfire.

He added the White House had worked with Reid and other senators “to ensure the prompt and fair consideration” of “nominees for a variety of important positions across the United States government.”

Max Stier, president of the Partnership for Public Service, said in an interview that lawmakers do not fully realize how the open posts affect agencies’ ability to function properly.

“I don’t think most of the political leadership in Congress understands how damaging that is,” Stier said. “It’s absolutely legitimate to hold the executive branch accountable if you give them the tools and resources they need. But if you don’t give them long-term budgets and leadership, then the blame’s on you.”

In some cases, the gaps are glaring. At one point the Energy Department had eight vacancies among its senior ranks, though it has gotten several nominees confirmed recently and now has three pending before the Senate. When Americans were panicked about the prospect of an Ebola outbreak in the United States, the White House could not deploy its surgeon general, since Vivek Murthy’s nomination had been stalled by the gun lobby. He was confirmed Monday night.

In the midst of the 2009 financial crisis, the Treasury Department lacked a confirmed undersecretary for domestic finance and an assistant secretary for tax policy. The administration has never had a confirmed head of the U.S. Mint, and the first permanent director of the Bureau of Alcohol, Tobacco, Firearms and Explosives, B. Todd Jones, was confirmed only in July 2013.

The fact that so many nominees now spend an extended period in limbo has also created a growing class of federal officials who are performing key functions without the same level of oversight and administrative authority as their Senate-confirmed counterparts.

Leslie Dach, who served most recently as executive vice president of corporate affairs for Wal-Mart Stores, joined the Department of Health and Human Services in July as a senior counselor. According to the agency’s Web site, “he works with the HHS senior leadership team on key policy challenges and strategic initiatives, as well on strengthening the Department’s relationships and engagement with external partners.”

This month, Education Secretary Arne Duncan announced he is bringing on former New York state education commissioner John King to serve as a senior adviser to manage the agency’s operations. And Vanita Gupta is serving as acting head of the Justice Department’s civil rights division; she is expected to be nominated early next year to be the office’s permanent head.

Sometimes the two parties can broker a deal. Sen. Marco Rubio (R-Fla.) put a hold on the Education Department’s nominees because he questioned the agency’s probe into a scholarship program for Florida students he championed; this month, the department concluded the decision to base student aid on standardized test scores did not violate federal anti-discrimination laws. Rubio has released his hold on James Cole Jr., who was confirmed Tuesday night after waiting a year and a half for a vote.

Several current and former administration officials, as well as some Democratic lawmakers, said the Presidential Personnel Office deserves some of the blame for the slow rate of appointments; Rep. James P. Moran (D-Va.) described it as “a black hole.” On occasion the administration has failed to line up a replacement for federal officials whose terms were set to expire, as in the case of former Internal Revenue Service commissioner Douglas H. Shulman.

And in a botched attempt to boost the morale of those whose nominations had stalled earlier this year, PPO Director Jonathan D. McBride sent them a form letter in May thanking them “for continuing to hang in there.”

Senate Democrats note that while triggering the “nuclear option” has alienated Republicans, it has helped usher some White House picks into office. Roughly a third of all the nominees confirmed since the rules change eliminating filibusters won approval with less than 60 votes, which would not have worked under the previous system.

And on Tuesday, the Senate confirmed Daniel J. Santos, after a more than 500-day wait, to take a seat on the Defense Nuclear Facilities Safety Board. The chamber approved not only controversial senior administration officials such as Sarah Saldaña, as head of Immigration and Customs Enforcement, and Antony Blinken, as deputy secretary of state, but also more than four dozen less contested nominees.

Earnest could not resist poking fun at Sen. Ted Cruz (R-Tex.), who created an opening for these nominees by demanding a vote on Obama’s recent executive action on immigration.

He noted that the “shenanigans” might have shown the junior senator had not mastered Senate floor procedure yet. “But we certainly are pleased with the outcome.”