The publication process has gone so far downhill it's basically not recognizable as science any more. This is driven by the university tenure process. Being a tenured professorship is a sweet job. The hours are short and flexible and the work is interesting and varied. Pay is less than industry, but once tenured the pay is guaranteed. Benefits are usually top-notch. That's an appealing package for anyone of reasonable intellect, middling ambition, and a desire for ironclad security. Not surprisingly, the supply of would-be professor labor greatly outstrips demand.
So who gets that cushy seat? Well, it's all based on publications and grant money. Grant money is based mostly on publications. So what you, would-be professor, need is a pile of publications. This is a huge change from the scientific publications of yore, which were by and large written for the benefit of the reader. These papers are written for the benefit of the WRITER, and that makes all the difference.
Most are on insanely obscure topics. The writer needs novelty (which is easiest achieved by obscurity) to get past peer review and no one cares if anyone else actually wants to know about the topic. Organization and clarity are for the birds - as long as the reviewers can't prove you're wrong per say it will get accepted somewhere eventually, especially at a pay journal. Reproducibility is actually undesirable - the last thing you want is scrutiny. It can't get you another publication, but it could force you to retract one. The problem being addressed by a given paper is typically very easy, but made to look very hard. Solve a hard problem, get one paper. Solve an easy problem that looks hard, get one paper. It's a no brainer.
Think these papers won't get past peer review? Think again. Mostly the journals don't REALLY read them. Just sort of skim. Think tenure committees will evaluate the papers on their merits? Think again. They don't have time, and in most universities the ultimate arbiter of tenure is the whole body of professors, most from different fields. TAre they're going to parse your obscure minutia? Heck no. They weigh it.
This can't be changed by fixing the journals. The real problem is that many of those publishing are doing so in bad faith. Right now scientists have exactly the journals they deserve.