Sisi ousted Morsi after he had been in power just one year on 3 July 2013 after mass street protests that followed strongman Hosni Mubarak’s ouster in 2011.
To justify their crackdown on dissent, supporters of the Egyptian military argue that they are facing a serious threat from a string of jihadist groups, demonstrated by a deadly attack in the North Sinai on Wednesday.
“The Sisi regime created the threats that it now faces,” said former US diplomat Michele Dunne, a Carnegie Endowment for International Peace scholar who was denied entry in Egypt in December. “President Sisi treats those who oppose the state [...] anyone who criticises the regime, anyone who demonstrates, is in effect treated the same way as those who use violence against the government. So they have created a very large pool of enemies.”
Hundreds have been killed and hundreds more sentenced to death after speedy trials targeting Morsi supporters. Morsi himself and several leaders of his Muslim Brotherhood movement are among those to have been handed the death penalty.
The repression, once limited to Morsi supporters and other Islamists, now also targets secular activists, including the now banned April 6 Youth Movement, which initially supported Sisi’s coup.
Rights advoctes say the rights abuses have reached – by Egyptian standards -- unprecedented level.
There are reports that 40,000 people have been detained, some of them still being held incommunicado. There are concerns that at least 160 arrests may be considered enforced disappearances.
"A generation of young Egyptian activists that came to the fore around the ousting of repressive ruler Hosni Mubarak in 2011 is today languishing behind bars," noted Amnesty International in a report aptly titled Generation Jail: Egypt’s Youth Go From Protest to Prison.
Shaimaa al-Sabbagh, a socialist activist and poet who was shot and killed while trying to lay a wreath of roses on Cairo’s Tahrir Square in January, embodies the regime’s poor rights record, according to Mohamed El Dahshan, a Cairo-based development economist.
“That is definitely for me a clear defining moment of what the government is like and how they plan to govern,” he said in an interview.
US Secretary of State John Kerry, expected in Cairo for bilateral talks on 28 July, is being urged by campaigners like Human Rights First, a New York- and Washington-based pressure group, to raise Egypt’s lacklustre record with his hosts.
“The United States has a strong interest in having a stable regional partner in Egypt, but President Sisi’s unprecedented repression, denial of rights and freedoms, and unfettered use of state violence is failing to restore stability,” it explained in a web article.
The murder of prosecutor general Hesham Barakat and the Sinai clashes earlier this week, a marked escalation of the violence in the Islamist camp, are likely to escalate the military’s response.
An infuriated Sisi has already called for fast-track executions of those on death row. the cabinet has already passed an anti-terror law to "achieve swift justice and revenge for our martyrs" – to the chagrin of advocates of due process.
“The fact that the president is instructing the judiciary is in itself an embarrassment,” economist El Dahshan lamented. “The executive shouldn’t be telling the judiciary what to do.”
The Islamists’ conservative social agenda and their power grab on Egypt’s institutions after Morsi’s massive electoral win in 2012 led the secular left to launch street protests that led the army to step in.
These demonstrations were organised by the Tamarod (rebellion) movement, which initially welcomed the Islamists' toppling by the military, even though this was the same army that had been the backbone of the Mubarak regime they detested.
Was Tamarod a genuine grassroots movement or was it infiltrated by Egypt’s "deep state" (sometimes described as a network of powerful insiders) and the security forces?
“There is a lot about Tamarod that is kind of fishy,” said Austin Mackell, an Australian reporter who was briefly jailed for his coverage of the unrest in Cairo. “There definitely was some involvement of the deep state. But I’m sure there were people [who] were not in any way working with the deep state [but] were coming into a political alliance with the forces of the old regime. I think there were a lot of people lying to themselves about it at the time.”
Sisi’s performance on the economic front has been markedly better.
Despite the unrest, Egypt’s economic growth is about five per cent per year, too little to make a difference, especially in impoverished rural areas, mainly due to 2.6 per cent population growth.
“What is needed is seven to eight per cent of growth, given the population growth," analyst Angus Blair told the AFP news agency.
Sisi is hoping to kick-start the economy with a nine-billion-dollar (eight-billion-euro) Suez canal expansion project scheduled to be inaugurated next month. It is part of an ambitious plan to more than double Suez revenues by turning it into an industrial and commercial hub by 2023.
But the inflation rate and budget deficit - 13.5 and 12 per cent respectively - remain key concerns.
Follow Michel Arseneault on Twitter @miko75011