When taking notes, it is possible to store notes of each type in a bespoke system that best suits the type of note. Web pages are stored as bookmarks in the browser, reading notes are stored as annotations in the PDF viewer, notes on videos are stored as–YouTube comments, maybe? This results in notes–which is to say, valuable information–being dispersed widely, rendering it difficult or impossible to find when needed.
A universal capture system instead offers a single place for notes of all kinds, either by being very simple, such a purely plaintext notes, or very complex (as with Evernote et al.), including special functionality to support capture of many kinds of media. The benefit, in either case, is that the capture process is simplified–you always capture all notes in the same way–and retrieval of any kind of note is possible without needing to first guess where to search.
In The Case Against Everything Buckets, Alex Payne argues, essentially, that computers are at their best when working with structured data, so we should store our data in specialized tools in order to take advantage of that. He's not wrong, but his argument isn't totally good, either. He says we're making computers work too hard:
So while you, the user, are presented with the illusion of “Googling” for that phone number you threw into your Everything Bucket, your computer is constantly hauling ass to make up for the fact that you couldn’t be bothered to put the phone number in your virtual address book. “What do I care how much work my computer does?” you say, until the next time the Spotlight indexer kicks in and your Mac grinds to a halt.
Sure, but that's more of a problem with the indexer than our use of unstructured data. We will have unstructured data, so our tools should be able to cope with it.
The general reply to Payne's objection is that just because you can put everything in a tool like Evernote, it doesn't necessarily follow that you should do that. Instead, you should use those tools for capturing all the stuff that, for your personal workflow, doesn't need to be in a more structured form. Then you (in theory) lose little by not using specialized applications, and gain the ease of universal capture and the convenience of having a single resource for all your miscellany.
John Gruber writes in Untitled Document Syndrome that reducing the friction involved in creating a new note is key. In his old system, using simple text files, but requiring him to manually create a file, pick a filename, and save the note, he created about one note per month. Using Yojimbo, a universal capture tool, he creates about one per day, which he attributes to the lack of friction.