There's not a lot of frippery in the office of Professor Ferdinand von Prondzynski, the principal of Robert Gordon University – there isn't a lot of frippery in the way he thinks and speaks either - but there are one or two little personal touches about the place and one of them is a picture of von Prondzynski with Hillary Clinton. The pair have known each other for years, ever since the professor's days as president of Dublin City University, and he has been out to visit her in the US several times. So I ask him what he makes of her chances of becoming president.

"A lot of people who know her from the media think she's slightly distant and cold," he says. "In fact, she's extremely warm. But that only comes out when you're in her company. I think she probably has the qualities to be president but she has to be able to communicate those. She is not always good at that."

It is a pretty honest assessment of his friend's chances of making it to the White House, but it also leads us directly on to the main reason I'm here to speak to von Prondzynski: his role as chair of what has turned out to be a controversial review of how Scottish universities are organised and run. Von Prondzynski says one of the aims of the review was to tackle something similar to the Clinton problem - a lack of public confidence – and his solutions were fundamental: elections for the chair of the governing bodies, greater involvement of students and trade unions, an end to bonuses for senior staff, among other reforms. The aim, says the professor, was to make universities more democratic, but also to achieve a higher level of public confidence.

The problem is that the plans, which are contained in the Higher Education Governance Bill currently going through Holyrood, have not been universally welcomed. Indeed, there has been some stern criticism from some of the 61-year-old professor's fellow principals. Professor Pete Downes, for instance, who is principal of Dundee University and convener of Universities Scotland, which represents principals, has said the changes will reduce universities' effectiveness.

Professor von Prondzynski's response to that is simple: show me the evidence. As far as he is concerned, the reforms address a profound problem: a lack of accountability. "As some people pointed out to me when I was chairing the review, universities' governing bodies uniquely in society are accountable to no one," he says. "They're not accountable to the wider population of staff and students, they're not accountable overall to the government, they're not accountable to anyone. But in a modern society, you can't have bodies taking fundamentally important decisions that affect both the institutions and the wider public without being accountable for it."

The negative reaction to some parts of the plan did not surprise the professor. "It doesn't surprise me because what we recommended was obviously a departure from the existing system, although not a radical one – the changes are not as radical as all the noise around them would suggest. But it was a departure and as with all change, you're probably likely to find those who have a stake in the status quo will resist it."

The professor also believes part of the explanation for the negative reactions to the plans is that the university sector thinks it's liberal but is actually conservative. "Universities are amongst the most conservative bodies you will ever find," he says, "they're full of people who are genuinely intellectual and clever and sometimes very liberal but in their own environment they're conservative. Some will say that's been a strength because universities haven't radically changed – as some people point out, universities and the Catholic Church are the only institutions that have survived intact since the middle ages."

He also insists that, despite the furore round the reforms, relations with his fellow principals are still good. "I don't believe this has ever become a personal issue – it certainly hasn't on my side – nor are any of the recommendations that we made in the review implied criticism of anyone in particular. I was always fully aware of the fact that almost whatever proposals we came up with would have been seen as difficult by some of the people who would be affected by them even if we'd decided that the status quo was the best thing and nothing should change – that would have annoyed the unions and some staff."

It's obvious the professor is relaxed about suggesting the reforms, and taking the criticism for them, but why is he like this? Here he is: a man in a senior role and someone who might be expected to defend the status quo and his part in it (which is worth a salary of £260,828 a year) and yet he's happy to question some of the fundamentals. He's also questioned whether we really need lectures in the digital age, for example, and he's even willing to think about whether universities need campuses (RGU has a rather neat and tidy one sloping down towards the River Dee). He thinks he's like this because he never wanted to be a university head and was pressurised into it at Dublin; he also says he's instinctively slightly anti-establishment despite the fact he comes from a very establishment background.

The background is an interesting mix: he was born in Germany but grew up largely in Ireland after his father, who was wounded in the German army during the Second World War, was told by his doctor to seek a quieter life. He chose Ireland, which meant that von Prondzynski was moved there when he was seven years old and grew up on a farm. He was a German boy, he didn't speak English and the Second World War was recent history (von Prondzynski moved to Ireland in the 60s) so life was tricky at first, and there was a bit of pressure, but von Prondzynski was fluent in English within a year and things settled down.

After six years in Ireland, the family then moved back to German although von Prondzynski returned when he was a student and has since lived all over the world, including Cambridge, the United States, Equador and now Aberdeen. Living in the city has meant that for half the week he lives apart from his wife and two sons who are still in Dublin, where his wife is a professor of English. During term time, she spends three or four days in Dublin and comes to Aberdeen for the weekend and once a month von Prondzynski does it the other way round.

The professor tells me, slightly sheepishly I think, that this means he and his family have three homes, which leads to the subject of how much he is paid. He accepts that the pay rises and bonuses received by university principals have damaged the reputation of the sector, but what about his own pay? Is he paid too much?

"That's a very difficult question to answer," he says, "because as you appreciate, it's not totally without a vested interest. I can't make that judgement about whether I'm paid too much but what I can say is that the process by which that question is answered needs to attract confidence.–If that question is both being asked and answered by people who are not disclosing why they are coming to the conclusion they are, or are not able to demonstrate the criteria they're using, and are not revealing anything about the process, then there's something that's wrong. There needs to be much more openness about how it's done."

As for bonuses, the professor thinks they should be essentially eliminated from universities. "A bonus culture in higher education is inappropriate – I'm not saying no one should ever get a bonus, but a) it should be relatively rare and b) there should be a very clear framework for assessing how that is justified, bearing in mind that when a university performs well, that's not just because one person has done something."

It's ideas like abolishing bonuses that probably help make von Prondzynski unpopular with other senior figures in universities but he has also been criticised for questioning free tuition fees and there are others still who won't like his public support for nationalism (he believes he was the only university principal to vote yes in the referendum last year). There is clearly an iconoclastic streak in von Prondzynski, which is why it is hard to pin down whether he's on the right or left politically. He says he has some sympathies with the libertarian outlook.

"Don't control everything," he says. "Let people develop freedom. I think individual freedom to do and say what you want is an important part of a free society."