When you see Egyptians vote, you can't help but be struck by the length of the lines and the fierceness of their internal debate.

At each stage, they seem to be taking their new-found stake in Egypt's transformation from dictatorship to democracy more seriously, displaying their views and their pride at the purple ink on their fingers more openly.

This weekend's two-day runoff election was supposed to be the last step in that historic shift, not just ending three decades under the thumb of Hosni Mubarak and the generals, but closing the book on eons of rule by pharaohs, kings and colonial powers.

On Saturday and Sunday, Egyptians will be voting for a new president who is supposed to take office by the end of the month, replacing the military council that has been running Egypt since Mubarak was deposed 16 months ago.

That's the plan, the grand dream that was championed by the many thousands in Tahrir Square, including the hundreds who died at the hands of police.

But it has been frustrated at every turn, often by the military council, and each step has left Egyptians bitter, divided and disillusioned.

Polarizing choices

After the initial round of presidential elections in May, Egypt's voters find themselves faced with two choices that could not be more polarizing or, for the revolutionaries in Tahrir Square, more depressing.

Anti-Shafiq demonstrators protest in Tahrir Square on June 8, saying they don't want to be ruled by another military man. (Suhaib Salem / Reuters)

On one hand, Ahmed Shafiq, Mubarak's last prime minister (very briefly) and a former cabinet minister who is the very embodiment of the old regime.

For many voters, particularly the well-off and religious minorities, he is an attractive candidate because of his promise to end months of messy street protests and bring Mubarak-like stability back to Egypt.

Those with different aspirations see Shafiq's candidacy as nothing more than a thinly veiled attempt by the old establishment — including the police and the military — to stay in control.

Shafiq finished second in the first round of presidential voting, with 23.7 percent, amid widespread rumours that hundreds of thousands of soldiers and police officers had been given cards allowing them to vote, contrary to Egyptian law.

But in a strange twist, he might yet be disqualified, if Egypt's Supreme Constitutional Court decides he is covered by the new law that seeks to bar all former Mubarak officials from running for office for a proscribed period.

Shafiq has continued campaigning as the court deliberates, though its verdict, which might come as early as this week, could throw the whole presidential race into question.

The Brotherhood's man

The other choice for Egyptian voters this weekend is Mohamed Morsi, the candidate who represents Egypt's oldest and biggest political movement: the Muslim Brotherhood.

Morsi narrowly won the first round, but not by dint of his charisma or any great vision for Egypt's future.

Personally, he's a bit of a mystery. But he was propelled by Islamist zeal and the organizational strength of the Brotherhood, with its unmatched roots — clinics, community centres and food banks — in every community.

In some poor neighbourhoods, bags of sugar or flour were handed out with a not-so-subtle message: Morsi's picture on the package.

The surprise of the first round was not so much that Morsi came in first, but that he didn't finish with more than 24.8 per cent of the vote.

This was far less than the 37.5 per cent support the Brotherhood had just received a few months earlier in the parliamentary elections.

Posters of the Muslim Brotherhood's presidential candidate Mohamed Morsi are displayed in a shopping area in Old Cairo. (Asmaa Waguih / Reuters)

In that intervening period, however, the movement squandered much of the trust it had gained from Egyptians looking for an alternative to the corrupt and oppressive Mubarak regime.

In these last months, the once-banned Brotherhood was now seen to be playing hardball politics, dominating parliament, entrenching its own patronage network and pushing a conservative Islamist agenda that Brotherhood candidates had steered away from on the campaign trail.

It was also accused of being opportunistic, withholding its support from the revolutionary forces until their success was clear.

The final straw for many here came when the Brotherhood decided to field its own presidential candidate, after vowing it would not. It had argued that one party should not control both the legislature and the presidency because that would give it too much power in the new Egypt.

Now it's on the verge of having exactly that power.

A question of legitimacy

With two such polarizing choices, it's little wonder that so many of the Tahrir revolutionaries, and many others, say they are planning to boycott this weekend's vote.

Several of the people they supported in the first round, more moderate candidates, some of whom received almost as many votes as the front-runners, are out of the running.

If the turnout is low enough, these groups argue, the new president won't have any legitimacy.

And that might not be the only institution in the "new Egypt" to suffer such a fate.

The country's top courts are considering the validity of the earlier parliamentary elections, which have been seriously challenged. The country has no new constitution (and the president-to-be still has no defined powers) because political parties couldn't agree on the makeup of the body that was supposed to draft the new order.

They're trying again now, though some MPs are boycotting the proceedings.

The generals

Meanwhile, Egypt's old institutions aren't getting much respect either.

Ahmed Shafiq talks during a news conference in Cairo June 3, 2012. He recently blamed his opponent for physical attacks on his campaign headquarters. (Amr Dalsh / Reuters)

They have refused to make any concessions to the changes sweeping the country and neither the courts nor the security establishment has been reformed in any significant way.

They are still run by judges, generals and police officials appointed under Mubarak, and are effectively the ones overseeing democratic change that threatens their power, prestige and pocketbooks.

Increasingly, the military seems to be entrenching itself as a fourth branch of government. Independent of any president, legislature, financial constraint or legal process.

It has dragged out the transfer of power and insisted on enshrining its political and economic privileges in the new constitution (it owns and runs several lucrative industries in Egypt).

If anything, the generals' use of intimidation has intensified. Under their continued rule, thousands of protestors have been arrested and tried in military courts with virtually no legal rights.

And yet, neither presidential candidate says he has any plans to rein in the military or make the generals accountable, a key obstacle to democracy.

Still, for all its obstacles, democracy is something that seems tantalizingly close to those in line at polling stations across Egypt.

As one voter, waiting on the outskirts of Cairo, put it: "We have so much we want to do and so much to wish for, but at least now we can start to wish. And I can start to do something here."