Prize-winning Freelance journalist Chris Barton said he left after a year last month due to work commitments, while Ellis has stood down after a period of poor health.
But Thompson's decision to stand down due to his then links with the Internet party has also created challenges for forming a Trust to try and obtain status as a charity. It was, said Barton, "not a good look".
If they can win charitable status and attract funding they may be able to finance public journalism projects that would not meet commercial priorities - but projects that the Trust regards as important to maintain democracy.
Public journalism funders like Pro-publica have become common overseas.
But the vision OF Public Eyes is still blurry.
Peter Griffin is a Fullbright-Harkness Fellow who has looked at in the future of journalism and resigned from Public Eyes about one month ago.
"I still think this type of venture is possible and there is more foundation money available that could be applied to something like this, he said. "But it will require the right mix of motivated people who are on the same page about what the best ways are to make the biggest impact with public interest journalism.
He said that one of the debates had been whether the foundation should support content for new media or if it wound up subsdising existing mainstream media.
Other key players remain such as business commentator Rod Oram and respected freelance journalist Alison McCullough, Stephen Olsen of the Newsroom organisation, and Margaret Thompson.
McCullough said the process had taken longer than expected.
A meeting in Wellington with like minded people associated with developing investigative journalism - including Nicky Hager and Massey University lecturer James Hollings - might help to define the way ahead.
Margaret Thompson - who is the mother of Alistair Thompson - said it had been difficult to maintain momentum due to the rigours of establishing the Trust.
She said the controversy over her son's past association with the Internet Party - before resigning from PublicEyes - had not affected progress for Public Eyes.
But Scoop has played a key role in the start of Public Eyes.
Thompson family interests dominate Scoop which has had a big role in the formation of the Public Interest Journalism Trust.
Scoop faces new challenges after millionaire Selwyn Pellet withdrew a capital injection offer for Scoop.
Rod Oram - a columnist for the Sunday Star Times - said he still backed the project.
The PublicEyes project was launched in November last year by co-spokespeople Alastair Thompson and Peter Griffin.
It was described as a call to action for people who would like to show their interest in becoming a trustee or a member of the planned editorial panel to put their names forward, or to nominate others.
"A key purpose of the trust will be to educate the public about the role and function of independent journalism in an open, democratic society and to fund reporting and journalistic investigation to that end" Alastair Thompson said.
