Conor Friedersdorf makes the case. Even if one concedes that an independent president would have a tough time initiating and passing major legislation:
Imagine a president who proved particularly adept at cutting waste from the bureaucracy while improving the performance of its various departments; who vetoed the most imprudent bills that the Congress passed, and signed the most carefully crafted, necessary legislation; who proved a competent steward of foreign policy, a talented diplomat, and an adept negotiator of advantageous treaties with other nations; and whose appointees to the federal bench had above average intellect, wisdom, and integrity.Well, yes. But here's the problem: a third-party or independent president would be in a poor position to do most of those things.
Could a third-party president do a good job of managing the bureaucracy? It's highly unlikely. The modern presidency has become a partisan presidency, in which presidents rely on partisan ties to staff the White House and the upper layers of the departments and agencies. And that's a good thing! Because the truth is that presidents have a hard time finding people to trust in those positions. Partisan ties don't just depend on loyalty; they also create incentives to people to do a good job so that they can be rewarded by the party in the future, either by moving on to more important jobs in the next administration or by going to work for party-aligned groups or think tanks.
See, any time that a president appoints someone to an executive branch job, there are at least three interests involved: those of the president, the agency, and the appointee. And while presidents should certainly be aggressive about monitoring what's happening, the truth is that they must rely on others to do much of that work, and they can't necessarily rely on those others, either. Partisanship doesn't entirely solve that problem, but it at least helps to align the interests of the president and political appointees.
So you're not going to squeeze a lot of waste out of agencies if the president's appointees go native and take the side of the permanent bureaucracy. You're not going to get a lot of brilliant diplomacy out of a president if the Secretary of State has his own delusions of grandeur and won't stay on the same page as her. And that's putting aside the severe problem of getting people confirmed in the Senate, a problem that might be even worse than it is now without having a party in Congress eager to help out a new president.