While the ruling National League for Democracy's (NLD) main candidate Htin Kyaw handily won the presidency in the parliamentary vote, the party's victory was just short of perfect.
Its other candidate Henry Van Thio in yesterday's vote managed only the second vice-presidency.
That leaves president-elect Htin Kyaw with the challenge of co-existing with first vice-president Myint Swe, the army's nominee.
The army also retains other powers, controlling 25 per cent of the Parliament and state assemblies and three key ministries - defence, home and border affairs.
All this could leave NLD leader Aung San Suu Kyi in a tough spot, said Dr Thitinan Pongsudhirak, director of the Institute of Security and International Studies at Chulalongkorn University in Bangkok.
Ms Suu Kyi, barred from the presidency under a clause in the junta-era Constitution, has said she will be above the president. That risks making the presidency look weak, Dr Thitinan said.
Additionally, while the vice-presidential roles are largely ceremonial, they do outrank ministers. In 2012, the then Vice-President resigned after some friction with President Thein Sein; he was seen to be stalling the President's reform efforts.
Managing working relationships thus will be critical, analysts say.
Indeed Ms Suu Kyi, as the de facto head of the government, would have to maintain a good working relationship not just with the trio of president and vice-presidents, but also with the commander-in- chief of the armed forces, Senior General Min Aung Hlaing.
Given that the party still intends to try to amend the Constitution and ease Ms Suu Kyi into the presidency - a move that would roll back the army's position - the civilian-military relationship will be critical.
"The army may need satisfactory assurances in respect of its priorities of national cohesion and internal security before it would contemplate constitutional amendments," Mr Trevor Wilson, a visiting fellow at the Australian National University, wrote last week in the online journal New Mandala.
Wrote historian and author Thant Myint-U: "The real transition we're going to see over the coming few weeks is not to a particular president or vice-president but to a government led by Daw Aung San Suu Kyi, something barely conceivable even a couple of years ago."
He added in an e-mail: "It will be a mixed civilian-military government and her authority will be hemmed in by constitutional constraints but she will wield real executive power for the first time."
He thought "the military will give the NLD considerable leeway on all issues they consider outside their national security ambit".
The key question then would be how much support Ms Suu Kyi would have, and how well she picked her Cabinet - which will be revealed next week.
Analysts say with her popular support she will have a significant honeymoon period even if expectations of the NLD government are very high. Yesterday, local media quoted Yangon residents, who avidly followed the vote on TV or social media, as voicing approval of her presidential choice.
"Of course the relationship between the president and vice-presidents will be significant as well, but far less so than they have been, because of her overarching authority over the vast majority of government," wrote Dr Thant Myint-U.