One big problem acadaemia has is the individual nature of research, even within research groups. A vast amount of time and effort is wasted on trivia due to working alone, which would be quickly resolved in a group. And while there is value in individual intellectual effort and reward, it can be vastly greater returns in a group context.
None of this is to say that lone investigation of out there ideas is bad. I think that's essential. But not for 100% of your time.
In many research settings, the scale of projects requires being a small part of a larger group. And while groups can squash good ideas, they can also kill bad ideas, and there needs to be a balance.
Not all PhD students are Einsteins, and it's as important to prevent people diving down a rabbit hole which leads nowhere as it is to give them the freedom to explore or else they might find they wasted several years rediscovering something already known or discovering nothing. I saw this happen to one of my fellows as well as myself. A good supervisor should be guiding appropriately. I found to my horror a PubMed search revealed a paper dating back to 1992 which had done several months of my research nearly two decades prior. When there are so many millions of papers, it's all to easy to miss stuff in the noise.
I'm skeptical of the calls to overhaul. Undergrads and even masters degrees went through this and now we have group projects and less individual learning. Too much focus on team work and collaboration. If anything we need to be teaching more wandering through the woods, more being on the out over the in of the group.
I would say there should be sort of a short PhD, maybe akin to MPhils, and ideally a step above the masters but below the PhD. The MPhils fulfil this ideal of more professionalized programs while PhD programs can remain more to their traditional styles.