Despite being praised for great leaps forward in democratic reform and economic development, Indonesia remains a country racked by religious intolerance, corruption and massive inequality.
In November 2010, US President Barack Obama returned to his boyhood home of Jakarta, stopping at the Istiqlal Mosque soon after touching down.
One of South-East Asia’s largest mosques, and sitting next to a Catholic church, it’s regarded as a symbol of diversity.
During his visit, the US president lauded Indonesia as a fine example of democracy and praised the country for its religious pluralism.
But within months, the world’s most populous Muslim nation would again be experiencing a surge in religious violence as 1500 people rampaged through the streets of Cikeusik in West Java.
Three worshippers from the Ahmadiyah Muslim minority group were clubbed and stoned to death. The horrific scenes which later aired on television showed police watching on, doing little to stop the carnage.
More than a dozen regional governments in Java went on to issue decrees banning members of the Ahmadiyah sect from openly practising their faith.
Just days later, mobs ransacked a court and burnt Christian churches in Temanggung in Central Java.
Two other key issues also remained constants: corruption and the threat of terrorism.
Before he first came to power in 2004, Indonesian President Susilo Bambang Yudhoyono had promised to stamp out corruption.
Now in his second and last term in office, his own Democratic Party has become the major source of scandal.
Stories of graft continue to dominate newspaper headlines with the Democratic Party’s former treasurer Muhammad Nazaruddin, who was apprehended in August after fleeing to Colombia.
Nazaruddin is accused of bribing other state officials to help a company win a RP 191 billion ($A21 million) contract to build the athletes’ village for the South East Asia Games.
Even the Corruption Eradication Commission has in turn been accused of corruption, ensuring the president has largely failed to bring about fundamental change in Indonesia in terms of the graft which for years has plagued the country.
The spectre of terrorism also continues to loom large over Indonesia.
There were some successes for authorities, including a conviction against Abu Bakar Bashir, who has long been suspected of an overarching role in the 2002 Bali bombing.
The so-called spiritual leader of militant Islam in Indonesia served almost 26 months for conspiracy over the 2002 nightclub attacks before being freed in 2006 and subsequently cleared of any involvement.
He was finally convicted in June, this time for funding a militant camp discovered in Aceh, and sentenced to 15 years.
However, nine years on from the 2002 Bali bombing – the country’s single deadliest terrorist act – the threat of further attacks remains ever-present, reinforced by the first-ever suicide bombing inside a mosque in Indonesia in April.
There were a string of other minor attacks, prompting concerns of a major shift in the style of threat from attacks carried out by organisations linked to groups such as al-Qaeda to “lone wolf” terrorism perpetrated by individuals or smaller cells.
Even the long-overdue conviction of Bashir lost some of its gloss when the High Court in October cut his sentence to just nine years.
While the Bali bombing remains a source of much pain for Australians, it is the constant flow of asylum seekers from Indonesia and the seemingly never-ending procession of Australians caught with drugs that provides much of the angst for Canberra.
Indonesia overwhelmingly remains the chief transit point for asylum seekers heading to Australia by boat.
The risk associated with the perilous voyage, demonstrated last year when up to 50 people were killed when their boat broke apart on rocks off Christmas Island, was echoed in November when as many as 15 people drowned after their vessel sank hours after leaving from a port in Java bound for Australia.
They kept coming in the last two months of the year, in spite of the onset of the monsoon season that makes the crossing to Australia even more treacherous.
Still, as so often is the case, it was the plight of just one Australian, as against that of many nameless asylum seekers, that grabbed the biggest headlines.
A 14-year-old schoolboy from Morisset Park, near Newcastle in NSW, became known as the “Bali boy” after being busted with about $25 worth of marijuana.
He was eventually sentenced to two months in prison on one count of “drug use” after telling the court he had been a long-term smoker of cannabis.
His case created a media frenzy, was discussed by prime minister Julia Gillard and President Yudhoyono, and led to the Australian Ambassador to Indonesia being told to make negotiations on behalf of the boy his top priority.
Other issues such as the suspension in June of the live cattle trade caused tension in the Australian and Indonesian relationship.