A military man or an Islamist fanatic? These were the two choices that the Egyptians were told they faced for 30 years under Mubarak rule. The ousted president, a former military man, often reminded the Egyptian people that it was either him or the Islamic fanaticism of the Muslim Brotherhood.

But finally, the January 25 Revolution erupted, a lot of blood was spilled, and many lives were lost. People thought that change was in the air. However, after Egypt held its historic presidential elections, there are some Egyptians simply dumbfounded to find that they have seemingly come full circle and are facing that exact scenario.

After a two-day poll for Egypt's top executive office, the presidential race is now between two men: a military man, in the form of former civil aviation minister Ahmed Shafiq, and the Muslim Brotherhood's candidate Mohamed Morsi.

For many of Egypt's revolutionaries, the choice is a repulsive one. Shafiq's victory was especially galling. He was hired by Mubarak in a last ditch attempt to curb the protests that erupted in Tahrir Square during the uprising. After Mubarak stepped down in February 2011, protests were held in Tahrir Square demanding that Shafiq step down. The protest succeeded and Shafiq resigned. The revolutionaries want to know how could a minister be ousted by revolutionaries, only to stand a good chance at becoming president 16 months later.

Ahmed Ezzat, a leftist activist and human rights lawyer, puts the blame on the Muslim Brotherhood. Ezzat points out that the Brotherhood were initially seen by the revolutionaries as an important facet of the January 25 revolution. But the relationship between the revolutionaries and the military council turned sour. And as time went by, the Brotherhood began siding repeatedly with the military on many issues much to the dismay of the revolutionaries.

"They sold the revolution and made deals with the council," fumes Ezzat. "These deals were for their interest and not that of the revolution."

This he points out, began with the March 19 referendum, in which Egyptians were asked to vote on the new constitutional amendments put forward by the military council.

The Brotherhood urged their followers to vote for Yes to the amendments, even though most of the revolutionaries were pushing for a No vote. In the end, the Yes vote won with 77% of the votes. Add to that, when the Brotherhood took 46% of the parliament, says Ezzat, they did not produce any legislation in favour of the revolution.

"The revolutionaries were demanding social justice, which was one of the pillars of the revolution and that the killers of the martyrs of the Egyptian revolution be put on trial," explains Ezzat. "But the parliament instead focused on talking about issues that are irrelevant to us."

He also blames the Brotherhood for allowing the elections to take place under military rule and the presence of Article 28 of the constitutional declaration which says that any decision made by the Supreme Presidential Elections Commission (SPEC) is final and cannot be appealed. This is compounded, Ezzat says, by the fact that Egypt still has no constitution and the powers of the incoming president remain unclear.

The Brotherhood's decision to contest the presidential race despite the fact that they were adamant that they would not contest in the first post-Mubarak elections, and going as far as firing one of their top leaders Abul-Fotouh, for wanting to run, was a source of dismay amongst many revolutionaries as well as some supporters of the Brotherhood. Ezzat says, that instead of producing Morsi as a candidate, they should have backed any of the two revolutionary candidates Abul-Fotouh or Nasserist Hamdeen Sabbahi.

"To refuse to support these two shows how utterly selfish they are," says Ezzat. "They were behaving as if these two were their enemies, when the real enemy here is the military council."

Beshoy Tamry, a revolutionary activist and a member of the Maspero Youth Union, tells Ahram Online that one problem that faced the Egyptian revolution, was the surge of Islamist parties, shortly after Mubarak stepped down in 2011. The Muslim Brotherhood which has been functioning for 80 years and was banned under the Mubarak regime got their licensed political party, the Freedom and Justice Party (FJP) immediately after the revolution. They were followed by other religious parties including the Salafist El Nour Party and El Asala Party.

"We should not have been silent about the creation of these parties, because they shifted the dividing point from whether you are pro-revolution or anti-revolution, to whether you want a civil state or an Islamic state," Tamry says.

Tamry also says that the Brotherhood is part of the counter-revolution, but the revolutionaries were fooled to think otherwise.

"While the revolutionaries were battling in the square during the 18-day uprising, the Brotherhood was holding meetings with Mubarak's hated intelligence chief, Omar Sulemian on 27 January, only three days after the revolution started," he says. "They also met with government officials again in February after the Battle of the Camel that killed so many Egyptians. So, when exactly were they with the revolution?"

Longtime activist Bahaa Saber, who was one of several revolutionaries to be summoned by the military prosecution last year, said that many Egyptians chose non-revolutionary figures, because the ruling military council has turned the people against the revolution. He wonders how the military council managed to secure the two-day presidential elections across 27 governorates, but failed to secure the country during the past 16 months. In fact, Egypt has been rocked by violence and clashes between protesters and the military several times in 2011. The violence also spilled in 2012 with the clashes that took place in front of the Ministry of Interior following the death of 74 football fans in Port Said and the latest flare of violence in the Cairo district of Abbassiya.

"Someone should ask that question," says Saber. "In my opinion, the constant violence of the last few months is one of the reasons why people turned their backs on the revolution. When you walk in the street, people are angry at the revolutionaries and beg us to let the wheel of production continue, which is brainwashing from the army."

However, revolutionaries have reacted in different ways to the election and the results. Prominent leftist political activist Wael Khalil, says that the Brotherhood and the Islamist trend as a whole have lost a lot of the popularity in the streets.

Although, final results are not yet out, Morsi received approximately 25 per cent of the vote, which is much less than the 46 per cent the FJP won during the parliamentary elections at the end of 2011. This, many analysts believe, is due to their poor performance in the parliament since it commenced.

"They worked with their full force, but were still punished electorally." says Khalil. "The surprise was Shafiq's stunning victory. We need to try and understand why that happened."

However, he concedes that the military council's anti-revolution rhetoric may have made Shafiq appealing to many.

"Shafiq's package, was not stability, it was to end the revolution and many people were attracted to that," says Khalil.

Add to that, the Egyptians failed to turn up to what was seen worldwide as one of the most historic days in the history of Egypt. Indeed, only 50 per cent of registered voters turned up.

"I think the problem is that many Egyptians don't feel that politics is related in any way to their livelihood," explains Khalil. "They think that they will live a miserable life no matter who is in charge."

Writer and thinker, Amile Amin, tells Ahram Online that the biggest drawback of the Egyptian revolution is that it never had a leadership. The revolution was initially triggered by youth, and for months after the uprising, Egyptians boasted that the revolution did not belong to anyone and was owned by all the Egyptian people. This, says Amin, turned out to be a problem.

"Any revolution needs a manifesto and a leadership," says Amin. "But the Egyptian revolution did not have either. It also did not have a vision. This made it easy for the biggest and most organised group, in this case political Islam, to hijack it."

Although there were attempts to unite behind a consensus revolutionary candidate, this never materialised. Notwithstanding the fact that the revolutionaries did not unite behind a single candidate, with many revolutionaries not mobilising for the elections at all, and the fact that the campaigns of those running on a pro-revolutionary platform were very under-resourced compared to those of the other contenders, in terms of numbers, the revolution did quite well. Many on microblogging website Twitter have noted that if the votes of Hamdeen Sabbahi and Abul-Fotouh are added together, the picture that emerges is quite different.

Now the revolutionaries are facing a major predicament with Morsi and Shafiq facing one another for the runoffs. Since the results were announced, many socialist and liberal forces, have begun urging people to back Islamist candidate Morsi in order to oust Shafiq, who they believe will bring Mubarak's regime back in full force.

Some analysts, however, see this emerging trend as disturbing.

"The Brotherhood was kicked out of the revolutionary forces. However, with the new results, many people want to make Morsi as the new face of the revolution vs Shafik who they see as the enemy of the revolution," says political analyst Sameh Fawzy.

The Brotherhood has actually begun appealing to all the country's forces to support Morsi in the second round to get rid of Shafiq. In a press conference on Friday night, the Brotherhood's Essam El-Erian, called for a meeting Saturday with the political forces including Sabbahi and Aboul-Fotouh to discuss a strategy for the runoffs in June. However, Fawzy does not seem too optimistic.

He says that this is a very dangerous political move from the seculars, who may be seeking something in return such as participating in the leadership of Egypt in the next few years.

"In turn, the Brotherhood needs to make some concessions for this support, but no they want it for free," says Fawzy. "This is very unsettling."