First we do not agree on free education. I believe that's a good thing.
Now, what Macron's government did wrong with research and higher education is: literally everything they did about it. The switch to high tuition as you said (especially given that it was only for foreigners, which I consider racist, and anyway the Conseil Constitutionnel recently found this measure unconstitutional). Parcoursup was a very bad decision: it is poorly designed, it is much worse than the previous system for university admissions for obvious algorithmic reasons that my undergrad students can spot (but that Villani apparently can't?), and it also does not solve the actual problem which is the lack of universities and professors. There is also the way they force universities to merge by making funding conditional to merger, this comes at high cost for no clear benefits (except for maybe jumping a _few_ places in the Shanghai university ranking, which is pure bullshit). There is the way they decided to fund public research: almost exclusively via calls for project, which is a very very inefficient wqy of distributing money as everyone has to work for month to make application and less than 10% of applicants are actually funded so more than 90% of all this work is done for next to nothing, and in addition to that the money is very badly distributed with very rich man that have so much money they don't even know how to spend it and a majority of labs where it becomes difficult to do any research at all. Their funding policy also force universities to cut there spending which is mostly salaries, meaning not replacing professors who retires for example, which means even less professors while there is more and more students (and that was forseeable, they all were born around two decades ago and have been through primary and middle and high school, we saw them coming). I could continue but I'm on my mobile phone so I will stop there.