What can academia do with the flood of bad or subpar paper currently online?
I strongly suspect that along with the papers being poorly formatted, they also have minimal usefulness content-wise.  I think the way to solve your problem is just to use a filter of only looking at papers in peer-reviewed, properly formatted journals.  And the better ones, at that.  

Yes, there is a possibility you miss something, but so what?  Euclidean perfection is not expected.  If you are doing original work, you only have limited time to spend on literature and you need to use that most efficiently.  Even if your sole task is to review the literature, you have limited time to do that.

If there is some work that was self published or poorly written but still important, than it should have been recognized (via citations) by papers in good journals.  (Then, recognizing the importance, you can spend the time to decipher the poor exposition...but again, this will be a tiny fraction.  Often zero.)

So, instead of worrying about academia (not a monolithic entity) somehow cleaning up the Augean stables for you (how would they even do that...take control of the Internet?), just change your own work habits to stay out of the muck or be very limited and targeted in your plunges into it.