U.S. President Barack Obama congratulated Indonesia’s President-elect Joko Widodo earlier this week and said the election outcome, in which Widodo defeated former army General Prabowo Subianto by about 8 million votes, indicates the commitment of the Indonesian people to democracy.

Peter McCawley, a longtime expert with the Australian National University’s (ANU) Indonesia Project, said, despite Prabowo Subianto’s intention to challenge the election results, Obama’s statement is an implicit endorsement of the outcome.

"No doubt the election was not 100 percent clean. There have been reports of hijinks (misconduct), games, of maneuvers on both sides. We need to emphasize that, on both sides,” McCawley said.

“By world standards,the election was surprisingly good. The election authorities in Indonesia were well-organized, the count was well-organized, and the ballot boxes have been protected. There is some dispute about some voting in some parts of Indonesia, but the best observers say any faults in the system are minor. And, they certainly do not undermine the overall result,” he added.

Comprehensive Partnership

The U.S. president reaffirmed the importance of “the close and cooperative relationship with Indonesia,” including the two countries’ Comprehensive Partnership.

Obama said he looked forward to meeting Widodo, widely known as Jokowi, and working with him to deepen ties and promote shared objectives.

Their first opportunity to meet may be in Myanmar, also known as Burma, during an East Asia summit in November. Widodo is to be inaugurated in October.

The U.S./Indonesia Comprehensive Partnership was officially launched during Obama’s visit to Jakarta in November 2010 and focuses on energy, security, trade and investment, democracy, civil society, education, and climate and environmental issues. McCawley said.

Across the board, the relationship has been good, although there are disagreements, he added.

"There is some concern, at present, about some policies at the Indonesian end about control of foreign investment. But this is the usual sort of push-and-pull in trade and investment matters between many countries and, in that area as well, the relationship is currently a strong and good one,” McCawley said. “There is, of course, the question now whether a new president brings changes of policies. But there is no sign that the new president is likely to do anything other than to continue this relationship."

Obama has tried to cultivate a closer U.S. relationship with incumbent President Susilo Bambang Yudhoyono as part of his administration’s rebalance to the Asia-Pacific region.

ANU analyst Greg Fealy said Indonesia is an important part of the U.S. rebalance because of its strategic location:

"It is the world’s largest archipelagic nation and it sits astride many of the major sea routes between the Indian Ocean and the Pacific Ocean and their important trade routes and, of course, military routes,” Fealy said. “It’s also important as the dominant country in the Association of Southeast Asian Nations (ASEAN).

“So, it’s very important for U.S. diplomacy in Southeast Asia to have Indonesia supporting its initiatives, and that gives a much better chance that other regional countries will also be collaborating with the United States,” Fealy added.

Human rights report

The 2013 U.S. human rights report criticized Indonesia for failing to conduct transparent and credible investigations into allegations of extrajudicial killings by security forces, and expressed concern about the lack of protection of the rights of religious and social minorities.

Fealy said the country’s human rights record should improve under Widodo.

"He’s very pluralistic in his orientation. We know that he got the vast majority of votes from the non-Muslim sections of the population, about 13 percent of the total population, and that shows that religious minorities trust him."

Fealy said Widodo has a track record, as governor of Jakarta and mayor of a major city in central Java, of being economically oriented. Widodo also knows that the success of his forthcoming administration will be in maintaining the country’s economic growth, Fealy said.