Peter Feaver at Foreign Policy has an excellent post on the dynamic between the U.S. and Europe:
But the truth is, the issues that bedevil Obama are the very same ones that bedeviled President Bush, and having a more popular leader at the top may not do much to change the underlying conflicts of interest.
On many issues, our European partners are more like "in-laws" than "allies." In-laws are people who share a common identity, even a shared long-term and enduring covenant, and this common identity is strong enough (usually) to outlast many frequent (and sometimes stormy) conflicts of interest. Allies submerge their conflicts of interests in order to accomplish an overriding goal, typically victory against a common enemy.
I think one of the big conceptual challenges in American foreign policy in the post Cold War era is internalizing the fact that without the Soviet Union to focus the mind, most countries aren't interested in subsuming their interests to Washington's decrees (this is now doubly true on economic policy, where Washington's credibility is at its nadir). We see this most clearly with Iran and North Korea, where other nations are putting their own interests (trade and regional stability) ahead of America's disarmament goals.
In an ideal situation, the U.S. would accommodate this divergence of interests by ceding security responsibility for nations like Iran and North Korea to the regional powers most directly at risk. If these powers still value trade with Iran or stability in North Korea over disarmament, then so be it. It's their neighborhood.