Most decisions made about the structure of PhD training are not made by random administrators like undergrad. The head of a program will be a faculty member in that department actively doing research and advising students, usually a faculty member that has been very successful in their research output (at least by official metrics). The decisions on how to structure first year curriculum, what to require for graduation, etc. are all made by PIs in that department.

Of course you are 100% right that those PIs are short term incentivized to keep the cheap labor coming. I think there's a decent chance that this utterly backfires on them in the next few decades, but I guess we will see. It has already started to backfire as far as obtaining postdocs goes.

Anyway, a small scale example of a better academic requirement IMO that would definitely be implementable by those making program decisions (because it already has at UCSD neurobio, perhaps elsewhere) is to change qualifying exams. In engineering programs I know quals involve grad level course work exams too so they're already a big time commitment, but in many bio programs it is simply a project proposal presentation and you get asked some questions on the background lit.

Because the project proposal is just a project you are planning to do in your lab for your PhD, it is not uncommon for it to be pre-scaffolded by the PI, not requiring original thought. At UCSD they require that you write your quals proposal/presentation on a different neurobio topic entirely from anything to do with your chosen lab. This makes it far more likely that students will put together an in depth scientific proposal themselves before embarking on executing what is often someone else's. Of course their proposal does not get implemented, it is just evaluated and given feedback by a committee of established faculty members.

However what I was getting at on a bigger level is that not all PhDs need specialized meta science skills, but some do. It doesn't have to happen overnight, but I'd like to see the process started by having some sort of branching in PhD requirements, perhaps like the quals change I described along with differing year 1 curriculums being optional. This shouldn't require many resources because at the graduate level it is completely fair game to stick some students in a room and give them some suggested references and a problem, and check back a month later. The important part is having not only the clear encouragement but also the protected time.

Oh and I think more opportunities to work with fellow students on meaningful projects is sorely needed too. PhD students from different labs mostly only help each other on a very surface level, it is rare to see students work together across labs in a way that each would be contributing authors on the other's paper. This has the opportunity to still be productive from a traditional viewpoint but also to naturally produce more thinking about a range of science.

Anyway, at a minimum I think professors can stop telling PhD students that e.g. wanting to attend a meta science reading group is a waste of time. Having that as a component of PhD education need not be compulsory or even expected, but for it to be culturally frowned upon is bizarre to me (though the selfish reasoning behind the attitude is obvious).

So the incentive structures part is again true, but incentive structures aren't going to change without an attitude shift and a willingness to diversify intellectually. And it kind of is chicken/egg - the incentive structures created a bad educational environment for some time now, and some of those people are already early career profs. They're in an even worse position to be trying to fix things because they're more ignorant of the fundamental problems to begin with. Seriously there are bad actors but there are also people that are just remarkably unaware of how to be remotely statistically rigorous for example. Either that or they are really good actors who are willing to look dumb in front of certain peers to further their long term goals, but academics don't strike me as the type to be content with playing dumb (if it's being perceived by others in any event).

Regardless, I'd be happy to start from a place of changing incentive structures if that were possible, and work from there. But at the end of the day I think this is an important factor for the incentive structures to consider. Bad training systems can create a real telephone game effect after a few generations.