Ahead of the vote, the overwhelmingly pro-el-Sissi media have been building a personality cult portraying him as the only man qualified to lead, while denouncing each potential challenger.
The allegations against General Sami Anan, a former armed forces chief of staff, mean that Sisi seems to be heading towards the March polls with most of his possible rivals already out of the running.
"People's confidence in the possibility of transforming electoral gains into a chance for a new beginning, has unfortunately, in our view, for now ended", Ali said at a news conference in central Cairo.
"Even numerous state's backers believe Annan's arrest was overkill", said Hani Sabra, founder of the consultancy Alef Strategies.
There were, he said, "signs that pointed to a will to poison the whole operation and to corrupt and empty it of its supposedly democratic content".
The arrests had started a few months "before we officially announced our intent to run... with some referred to urgent trials", said Ali, who had announced his intention to run in the race in November.
If his conviction is upheld on appeal, Ali would be ineligible to run.
Under the constitution, would-be candidates must obtain 25,000 recommendations from voters or secure the support of 20 elected lawmakers to qualify to run.
Abou Shaqa was appointed his legal representative, as well as the official spokesmen of the campaign, said the president on his official Facebook page.
That paves the way for President Abdel-fattah al-Sisi to run for a second term in March without any major challengers.
Veteran air forces commander and former Prime Minister Ahmed Shafiq, who fled Egypt after narrowly losing to Morsi in the 2012 elections, announced earlier in January his withdrawal from the presidential race after coming back to Egypt from the United Arab Emirates, where he spent the past five years. The arrest was also confirmed by two of Annan's aides, Mustapha al-Shall to the AP and Mahmoud Refaat on Twitter. Last week, el-Sissi unexpectedly fired his spy chief, who had been considered a close ally.
"This is consistent with the Egyptian government's ongoing efforts to crush dissent and consolidate power by attacking civil society, activists and human rights defenders in the country".
In his first public comments since Annan's arrest, el-Sissi on Wednesday reiterated vague warnings that Egypt is the target of a foreign conspiracy.
Anan went on to cite "erroneous policies", which, he said, had forced Egypt's military to bear numerous responsibilities traditionally borne by Egypt's civil sector. "No one (should) make us go astray", he said.
He also took the unusual step of appealing to the military and state institutions to remain neutral in the election, saying they should not be biased in favor of el-Sissi.