In my limited experience as a disillusioned PhD student dropout, the issues are in approximate order:

1. Publications in prestigious journals have become a measure, not a way to communicate. This leads to perverse behavior.

Any kind of project that would involve deep work is very scary, unless it has early low-hanging fruit called easy publishable papers as intermediate steps that are easily published. I personally felt I was encouraged to find such fruits without too much coherence in what I was doing. Preferentially one does not have to learn or study anything challenging, because that makes the fruit potentially much more difficult to pick.

My proposed solution: do not judge researchers by length of their publication list to evaluate them to hire/fund. Judge them by a selection of their recent work instead and maybe their presentation what they are doing now.

2. This is connected to another problem, corrective feedback comes quite late into play, when the most work has been done and it is very costly to change anything. I feel better results could be had of reviewers entered the stage when study was being drafted.

Currently, submit a manuscript into a journal, get it rejected after a round of substantive, critical but correct reviewer comments? Optimal thing is not to review the work as suggested in the light of new ideas, but try to find a less prestigious journal likely to accept it with minimal work.

3. This has effects on conferences. While their primary purpose has always been presenting ones research and hearing about others, they kind of turn too much into a platform for advertising your research so that you get cited. Thus the general feeling can be quite one-way, and there is less knowledge enhancing communication by scientific discussion. Some conferences are better than others (amount genuine curiosity and interest helps), but sometimes I felt people would come to deliver their own little advert, maybe as chore between meeting their personal friends, instead of coming to talk, both receive and offer meaningful updates.

4. PI-centered networks and death of university department. I believe originally university departments were formed because it was thought beneficial and reasonable to have scholars with similar interests nearby. Social networks are probably quite important part of science, and is easier with people who are located often in the same building. Research group culture is a fascinating way to have groups of people nearby who don't communicate. It appears that to PI, each unsanctioned contact from their underlings to outside the group is a distraction at best (if it leads to underling working on publishing something PI is not involved in) or an unwelcome threat at worst, because it risks changing their plans, whether they concern the projects underlings should working on, the author order on planned manuscripts, or something else. All presentations to group outsiders is about signalling importance, prestige and coolness, but no research communication within department to help with unfinished work.

Solution would involve stopping funding faux institutions within institutions, and start paying researchers in a way that encourages them actually collaborate within their physical departments when it is useful. (Salary paid by university/dept., no project grants.)

5. I suppose science moving very large projects involving lots of contributors can not be helped, but it is incompatible with publication authorship as the currency of value in academia. It leads to authorship beimg traded as a currency within projects. One is "paid" by official authorship in some papers; sometimes a person can show their magnanimity by bestowing it upon some people who participated. Sometimes technical or statistical help does not get acknowledged.

IDK what to do about that. Moving out of evaluating publication lists to evaluating personal contribution/capability might help. In addition to big publications that are meant to communicate the big findings publicly but leave outsiders to interpret author order like tea leaves, record publicly some documentation what exactly each individual did, in their own writing, and that documentation is what the contributors should refer to in their CVs?