It's possible for 90% of papers to be rubbish without any ill intent or dishonesty on the part of the experimenter. They might simply suffer from "works for me" syndrome, as it afflicts software developers. In science, this equates to failing to control for all the possible confounding factors that might affect the result of the experiment. They might have carefully controlled for everything they thought of and gotten methodologically valid results, but then when another experimenter tries to replicate it, they find their experimental environment is different in a way that neither considered important but alters the results.
Finding all these conflaters is the point of science. If you can't replicate the experiment, it means the results don't hold, but it doesn't mean the investigators were bad people - and assuming they are is unlikely to get better science.
New business ventures are inherently risky.
Research is inherently risky, and we would expect 90% to 'fail' but for 90% of papers to be rubbish would be a matter of 'extreme corruption' along the lines of 90% of judges taking bribes etc..
"I don't see a better system."
Well, one thing we could do is punish people for knowingly publishing crap results, i.e. have a 'secondary review system' that investigates 'why' results were rubbish, and if there was malfeasance, well, put in place some kind of retribution.
We could also change our tune with respect to expectations, and come to 'expect' that the majority of research should publish then 'null' result and that should just be it.