Now that the media module is in core (watch our class on the Media Module here), we're starting to see some contributed modules come along that help fill in some of the gaps. Not being able to replace an image, pdf, or video is one of the most notable issues with the Media module.
So if you had a PDF that gets occasional updates, the only recourse you would have is to upload a new version and then head over to every node where the pdf is used and change it out. There has to be a better way!
Well, now there is: the Media Entity File Replace module from Brian Osborne.