For the state, it seems, the strategy developed by Mr. Kaloyeros and trumpeted by Mr. Cuomo — to lavish hundreds of millions of dollars in state subsidies on corporate partners to create high-tech jobs — is unblemished. Yet the model has come in for repeated criticism from government watchdogs, who say an economic policy that tries to create risky new industries virtually from scratch, and that spends millions in taxpayer dollars to create every new job, is folly.

“We’re incredibly skeptical of the economic logic behind these projects because they’re too expensive,” said John Kaehny, the executive director of Reinvent Albany, a good-government group. “There is no economic logic to this, really. But there’s a huge political logic to it. The governor desperately needs for this to be a success for his political legacy in New York.”

Local officials have praised Mr. Zemsky as an inclusive and open manager. For those who watched the Utica deal crumble, however, his involvement was a belated acknowledgment that the state could have done better from the beginning — and been better attuned to signs that the program was ailing months before the indictments made it obvious.

“Shifting blame to the procurement process at SUNY Poly is drawing attention away from all the missed opportunities the governor’s office had to step in and make sure the AMS project was moving forward,” said Assemblyman Anthony Brindisi, a Democrat from Utica. “I think the governor’s office, essentially, when it came to economic development upstate, turned the keys over to Alain Kaloyeros, and unfortunately in the case of Utica, Alain drove the bus right off the cliff.”

Mr. Cuomo’s aides reject the idea that the state has lost credibility in its efforts to revive the upstate economy, saying their economic development efforts were always much bigger than the ones Mr. Kaloyeros oversaw.

“SUNY Poly’s narrowly focused on some very high-profile tech projects, but for someone to say economic development, broadly speaking, has been turned over to to someone at SUNY Poly is just incorrect,” Mr. Zemsky said, citing the governor’s efforts to involve regional officials in economic planning and to spread state funds across thousands of smaller economic development projects.

He said he was confident that they would ultimately bring the nanotechnology projects to fruition.

“That is the only thing, at the end of the day, that can change that taste in people’s mouths,” he said.