When he started out in his career, people with dementia were routinely strapped in chairs all day and patients admitted to hospital care were often allowed to wear only their pyjamas until considered to be "safe".
Yet, over the past decade as chief executive of the Mental Welfare Commission (MWC) for Scotland, despite much progress, several of the cases Dr Lyons and his staff have had to report on were harrowing in the extreme.
They include that of Miss X, who had learning difficulties and was raped and tortured by three men - one her carer - while in the care of the Scottish Borders Council and NHS Borders. There was also Mrs V, an 80-year-old with dementia whose treatment at Ninewells Hospital, Dundee, was deemed degrading and "unnecessary".
The MWC's investigations on both, published in 2004 and 2011, were highly critical and helped prompt major reviews and inspections of the treatment of vulnerable adults.
"If the commission lost its sense of outrage at situations where things have gone badly wrong for people when professionals have not offered the care that should have been offered… there is no point in us being there," said Dr Lyons.
"We are there to shine a light on good practice, but also to learn when things have gone wrong. I would much rather do the former, but when things go wrong we have to make a noise about it. We have to make things better ."
Dr Lyons, 55, who is married with three grown up sons, was born and raised in Gourock, Inverclyde, and after studying medicine decided to specialise in psychiatry. He was appointed a consultant psychiatrist at Leverndale Hospital, Glasgow, in 1989, specialising in treating patients with dementia where he worked until he became the head of the Scottish MWC in 2003.
He steps down from his post as chief executive of the watchdog next month, to be succeeded in April by Colin McKay, a senior Scottish civil servant.
Dr Lyons says the highlight of his tenure was addressing a UN committee in Geneva last June on UK developments on safeguards to patients in detention from ill-treatment.
Closer to home, he also cites, half-jokingly, being called in to offer script advice on a storyline about a character with a mental health problem on the BBC drama Waterloo Road, set in his old school, Greenock Academy.
Over the past 14 years a raft of new laws - including the Adults With Incapacity (Scotland) Act 2000, the Mental Health Act (Care and Treatment) (Scotland) 2003 and the Adult Support and Protection (Scotland) Act 2007 - ushered in vast changes, giving more rights to patients, setting out more protections from ill-treatment and giving them more of a voice. Part of Dr Lyons's job has involved monitoring this new legislation in practice.
The Mental Health Act also introduced community-based compulsory treatment orders, which allow patients to be treated at home, as well as advance statements, which enable people with longstanding mental health problems to set out how they would like to be treated if they become acutely unwell.
One of the biggest changes introduced by the Act was the establishment of mental health tribunals, where appeals against compulsory orders are heard. Previously appeals were made at the Sheriff Court, making those taking the appeal feel like a person accused of a crime.
Dr Lyons believes that as a consequence of these changes being implemented Scotland now leads the world in many respects in terms of its mental health system. "I think mental health care has come on a long way in Scotland over the past decade," he said. "There has been a shift in the culture of doing things to people with mental health issues to doing things with people.
"On the international stage the mental health service in Scotland has punched well above its weight. The legislation we have is being looked at worldwide."
Despite the progress made, Dr Lyons says there are still aspects that need to improve.
Top of the list is the standard of hospital buildings and accommodation in some of the country's main psychiatric institutions, which he describes as "outdated and shameful".
"The fact we have some very outdated in-patient mental health facilities in Scotland is shameful," he said.
"There are parts of Stratheden Hospital in Fife and the Royal Edinburgh Hospital, to give examples, and they are not the only ones, where the fabric of the buildings is so outdated that we have arranged on-sites visits with the chief executive.
"In both cases we are very pleased the chief executives have acted when the issues have been brought to their attention and brought forward dates for improvements."
Another continuing issue is the persistence of poor attitudes to patients in some settings.
"You can have isolated groups of staff who go their own way, who do not respect the individual as they should," he said. "You can get an insular culture in some places where people on the inside have to fit into that group. I have seen that in remote rural areas and have also seen it in big cities. They are stuck in a way of thinking that belongs 20 or 30 years ago."
A third area for improvement is in the provision for in-patient treatment for young people with serious mental illnesses which sees some having to be admitted to adult wards.
Dr Lyons says provision varies across the country. For instance, in Edinburgh and Fife very few young people will be admitted to adult wards, with the vast majority being treated in specialist young people's units. However, in other areas, notably Greater Glasgow and Clyde, Lanarkshire and the Forth Valley a lot of young people are being admitted to adult wards.
These shortcomings in the services are, no doubt, issues Dr Lyons' successor will take up.
But while Dr Lyons is stepping down from the high-profile role - no doubt relishing the chance to spend more time supporting Morton FC - he plans to continue his work in the field of mental health.
"I have had a very rewarding career in mental health and am not giving all of that up," he said. "I hope to keep up my involvement with a number of mental health charities and keep in touch with the Mental Welfare Commission."