The purpose of Let's Encrypt, and the SSL certificate infrastructure in general, isn't to prevent "bad guys" from getting certificates. It's to ensure that if you own the box, the certificate verifies that a web client is speaking directly to that box with nothing in between. (Or more generally, directly to an authorized end point by the owner of that DNS entry. Authority can be delegated.)
In other words, it keeps bad guys out of the middle, not the end point. That's all SSL can do, even if it works perfectly. Bad guys will still own end points, in both the conventional sense of the word own and the pwning sense of the word own. SSL can not (directly) do much about that. If you speak SSL to a bad actor, well, there aren't any other actors between you and the bad actor, but you're still speaking on an encrypted, authenticated channel to a bad actor.
This is in contrast to the DNS infrastructure in which it is sensible for a TLD owner to attempt to prevent "people they don't want on their TLD" (more generally than "bad guys" since a lot of the restrictions enforced are far beyond that).