"This quarter was undoubtedly worse than expected, with an industrial result that was worse than what we saw in March 2007, preceding the financial crisis," J.P. Morgan analyst Stephen Tusa wrote in a note Friday.
The firm says GE's businesses "are impaired," citing the continued generation of "essentially zero" free cash flow. J.P. Morgan does not see GE's management as leading a simple restructure of the company. Instead, J.P. Morgan says Flannery and others are "fighting to salvage value."
"The bottom line is that there are more questions than answers here," Tusa said.
Investors are looking to November, when the company provides more detail about its expectations as it works to reshape its business. But the disappointing quarter and a reduced profit forecast tested investor patience Friday. The earnings miss was the company's biggest in at least the last 17 years, according to Bespoke Investment Group. Prior to Friday's report, the company's biggest miss relative to Wall Street expectations was just 7 cents, in April 2008, according to Bespoke's Paul Hickey.
After stripping out restructuring charges, GE earned 29 cents per share from continuing operations in the third quarter, down 9 percent from the same period a year earlier. Analysts surveyed by Thomson Reuters expected the company to earn 49 cents per share.
GE revenue rose 14 percent to $33.47 billion, which beat analysts' expectations of $32.56 billion.
The company cut its forecast for the year, lowering estimates for its 2017 adjusted earnings per share to a range of $1.05-$1.10, from $1.60-$1.70.
GE's performance was weighed down heavily by its power business, which saw profits decline 51 percent to $611 million, from $1.3 billion at the same time last year.
The company also posted a loss at its oil and gas business. It swung to a loss of $36 million from a profit of $353 million a year ago.
"We are focused on redefining our culture, running our businesses better, and reducing our complexity," Flannery said in a statement. "I look forward to meeting with investors in November to update them on our progress."
The company has seen sweeping personnel changes, including the departure of its CFO, the earlier-than-expected retirement of its chairman and the addition of Trian Partners CIO Ed Garden to the board.
Trian's Nelson Peltz told CNBC earlier this month that he had pushed to get Garden on the GE board to "bring a fresh mindset." GE is considering extensive cost-cutting measures, and Peltz said "everything is on the table."
"Hopefully, that company will start to run the right way and the board will get more active," Peltz said.
Trian Partners has a $1.6 billion stake in GE, according to FactSet.
GE stock has declined by more than 25 percent this year, as of Thursday's close at $23.58 per share.