Richard Skinner, a visiting assistant professor of political science at Bowdoin College, sent me his new Political Science Quarterly piece "George W. Bush and the Partisan Presidency" (sub. req.), which does a nice job of synthesizing the evidence that the relationship of presidents to the party system has changed in the contemporary era. The traditional literature on the presidency saw the "modern presidency" as standing somewhat apart from the party system, a description that applies reasonably well to the period of the 1950s-1970s. However, Skinner argues that the model has changed since Ronald Reagan. "Partisan presidents," including especially George W. Bush, are closely aligned with their party in Congress, tend to face a relatively unified opposition, and take a partisan approach to staffing the executive branch.
It's easy to see this shift as a turn for the worse; David Broder and other establishment pundits frequently bemoan the decline of Congressional and executive bipartisanship. But it's worth noting (again) that the politics of that era were less polarized as a result of the suppression of the issue of race, which kept southern conservatives in the Democratic party while splitting it along regional lines. Once the parties diverged on racial issues during the civil rights era, the political system returned to a more normal state of affairs.
Understanding the change in this way reveals a paradox -- the civil rights movement that made Barack Obama's ascension to the presidency possible also set in motion a change in party alignment that will make it impossible for him to fulfill his promise to bring the parties together (as in the House stimulus vote today).