President Barack Obama and Premier Benjamin Netanyahu made it through their first official meeting with no apparent harm done to US-Israel comity. But their careful language about shared threat perceptions and deep historic ties did little to disguise the obvious: there are interesting and difficult challenges ahead as Israel and the United States, separately and together, approach the enduring quest for peace and security in the Middle East.

First, the two leaders are in different places politically. Obama enjoys enormous popularity and legitimacy at home and abroad. He is at the beginning of his presidency and is buoyed by goodwill from many sides, despite the gravity of the world economic crisis for which he has special leadership responsibilities. Netanyahu is no novice in his job, and voters in Israel and observers outside are far more cynical about his capacity to be a positive agent for change. He himself is likely to be more focused on keeping his unruly coalition together and will be more tactical in his thinking than Obama.

Second, there's the well-trodden ground of whether they actually share a vision for a two-state solution. Obama, accepting the accumulated wisdom of American experts, thinks of an independent Palestine as a positive and desirable outcome; for Netanyahu it's perhaps one of the less bad options, but around him are political partners who quite passionately oppose it. There are clearly divergent views about how much effort to put into improving Palestinian morale, building Palestinian capacity for governance and security, and demonstrating respect for Palestinian identity. The Israeli leader seems to think that more flexibility on economic transactions, including trade and employment, is the right amount of attention. For the US, that's only a piece of a larger set of initiatives and activities.

Third is the dilemma of what to do about Iran. Obama has set some ambitious goals for his administration and is open to a very different way of doing business with Iran. He's trying to change the tone and the underlying psychology of the long-standing antagonistic relationship. He wants Iran's leadership to believe that a more productive interaction with Washington is possible - one that would have economic, social and security benefits for Iran and would defuse tensions in the region, to the benefit of all.

Israel is coming from a very different place: its leadership does not see Iran as a normal country but as an existential threat. The notion that Obama is willing to take risks and to attempt to build trust with Tehran is quite outside mainstream political thinking in Israel (although a few independent intellectuals can still envision a return to normal state-to-state relations between Israel and Iran).

The US and Israel have had countless exchanges of information, intelligence and policy ideas on Iran's nuclear program. But Netanyahu and Israel's supporters are concerned that Obama is embarked on a divergent path that could include a deal on Iran's enrichment activities, putting the two countries on different sides of the line of what is acceptable.

A last and more philosophical issue is Obama's commitment to improving America's engagement with the Muslim world. His upcoming speech in Cairo will surely lay out a positive vision of a multicultural world of tolerance and mutual respect. Obama embodies an openness of mind and spirit about coexistence. Americans have high hopes for his ability to help repair the damage done during the Bush era to America's reputation and to reverse the perception that the war on terror is in fact a war against Islam.

One senses that the mood in Israel is quite different; Israelis are disheartened and despairing of ever achieving normal relations with their Arab and Muslim neighbors, and seek assurances from their US partner and patron that American security policies will take into account this deep sense of vulnerability. But some will see Israel's predicament as one that only the Israelis themselves can resolve. The fact that Israeli Arabs, long seen as the quiet beneficiaries of life in a vibrant democracy, tell pollsters of their deep alienation, is disturbing. It is part of a larger piece of Israel's enduring failure to make coexistence possible and desirable for the Arabs. This is a very local process, less susceptible to outside influence or direction.

Most of the pundits think the first Obama-Netanyahu visit went just fine, with Obama doing what he needed to do on settlements and Netanyahu making clear his expectations that the US overture to Iran be limited or bound in time. But it's important to not be distracted by a fairly superficial reading of the situation: Obama is thinking strategically about how to reset the agenda for the region. He sees the connectedness of issues in a positive-sum way. Israel's leaders should be listening carefully.