They say his decision to have a single management team, headed by himself, running all Jet's operations was a crucial mistake.
Analysts say he should have had one team running the full-service carrier and another running the budget flyer.
"Jet lacked a concrete business model and fiddled with it often, which confused investors, (and) passengers alike," said Agarwal, who believes the company's decisions lacked transparency.
Goyal has also been accused of making bad investments and failing to address the company's deteriorating financial predicament while borrowing heavily.
"Simply put, they spent more than they earned and kept accruing debts," added Agarwal.
All of India's carriers are particularly sensitive to fluctuations in global crude prices because the Asian giant is a major importer of oil.
When the rupee is weak, which it has often been over the past year or so, fuel -- the biggest cost burden for airlines -- becomes more expensive.
Soaring oil costs and the Indian rupee hitting record lows last year affected all Indian carriers.
IndiGo and SpiceJet reported massive losses but analysts say their books were resilient enough to weather the quarterly losses. Jet's, however, were saddled with debts.
"Jet Airways failed to manage its balance sheets and was caught out by these cyclical changes in the industry," Mumbai-based economist Ashutosh Datar told AFP.
Aviation analysts say Goyal's failure to find a strategic investor to pump money into Jet extended the airline's losses, contributing to the financial predicament it finds itself in today.
Talks at the end of last year with tea-to-steel conglomerate Tata failed to go anywhere, while Etihad Airways reportedly refused to increase its stake because Goyal was at the helm.
The 69-year-old was forced to give up control of Jet last month as part of a debt resolution deal that saw a consortium of lenders led by the State Bank of India (SBI) take over the airline.
It is now up to them to find a buyer. If they don't then Jet is likely to become the first Indian airline to collapse since fugitive tycoon Vijay Mallya's Kingfisher Airlines ceased operations in 2012.