Either Hosni Mubarak’s last prime minister or the Muslim Brotherhood’s (MB) candidate is set to be Egypt’s president following a runoff election, but the powerful role the military is set to retain remains a cause for concern.

The election is the result of last year’s revolution, which led to Mubarak’s ouster after a 30-year rule. By and large, those who took a leading role in the revolution were secular Egyptians opposed to Mubarak’s dictatorial rule; the Muslim Brotherhood largely remained at the sidelines.

That a Mubarak ally and the Brotherhood’s candidate qualified for the runoff election may leave many to feel cheated. However, the result of the first round of the presidential election is very much plausible, even though claims of voting irregularities have been made by a number of candidates.

The two leading candidates – former prime minister Ahmed Shafiq and MB-affiliated Freedom and Justice Party chairman Morsi – benefited from being associated with Egypt’s largest and well-organised political organisations, even though Mubarak’s National Democratic Party has been dissolved.

Many activists had even suggested that the election be delayed further to help diminish this advantage, but such calls were unsuccessful, and the vote of those opposed to either frontrunner was ultimately split among a number of candidates.

However, even if one takes the most sceptical view of both Shafiq and Morsi, there may be a bigger problem for Egyptians to overcome as they seek to develop a democratic system: The country’s powerful armed forces.

The Supreme Council of the Armed Forces (SCAF) assumed power in the wake of Mubarak’s resignation to oversee a transition period, but criticism of the ruling junta has been increasing. It has itself resorted to using force to quash continuing protests, tried thousands in military tribunals and arrested critics.

The future president’s powers, in relation to the military, are also yet to be determined, and SCAF appears to be striving to maintain the army’s powerful status as an entity effectively independent from the government. Its main demands are that the government cannot declare war without its consent and, citing state security reasons, that its budget remains a secret.

The army actually controls a sizeable proportion of Egypt’s economic production – up to a third according to some estimates. If the situation persists and its demands are met, a civilian government would have little, if any, ability to rein it in.

In this regard, it might be hoping to emulate its Turkish counterpart, which has carried out three coups d’état and helped oust another prime minister since 1960, although its power has since decreased as the country strives to join the EU. The situation would be far from ideal for a budding democracy.

Further complicating matters is the constitutional assembly, which is dominated by Islamists and boycotted by a number of liberal and secular parties and which has been suspended by a court order, elected to form a new constitution.

Encouraging news did arrive last week, when a state of emergency which had been in place for 31 years was lifted. And obviously, the fact that millions of Egyptians are voting in an election where the outcome is not a foregone conclusion is an obvious sign of improvement.

But that the process to forge a healthy and vibrant democracy will not be an easy one is an understatement.