The main problem I was having with Evernote was the inability to archive on a separate drive. In the past I was enthused that Evernote could be used to store much more than text notes and so I accumulated, over many years, more GB of notes than I wanted to store on, for example, a Microsoft Surface. I had lots of very large PDFs. Other systems, such as OneNote and TagSpaces are not dependent on everything being held in a single file structure like Evernote required in Windows desktop (but perhaps that has changed recently? I haven't kept up with Evernote recently).
A secondary problem was quickly searching only non-archived notes.
And then as my problems with archiving grew I realised possibly the biggest problem - so much of what I had was tied up in a proprietary meta-data and storage system. So I've since back-peddled (avoiding OneNote* as well, though I think Microsoft have quietly made that better and better over the years) and have gone for a much simpler tagging system that allows me to keep all notes in native formats that will never be tied to any one storage 'system' (TagSpaces simply adds tags to filenames - it has some nice Open Source software to create, tag and find files but you can also just use any standard file system if you needed to; it's a very very simple idea).
But I also don't agree with you when you say "Evernote’s methododology is organization by Tags, instead of the traditional folder/subfolder methodology". It has both a folder structure and a tag system. I liked (and still like) the combination of having both a tree (folder) and tree-less (tag) system. The advantage of a file structure is that I can very easily move a whole folder (usually a project) over to an archive drive, and I can specifically share folders when I work with other people on a project. So, for example, using DropBox (with files tagged by TagSpaces) when I finish on a project I move it to an archive folder. That keeps it in DropBox but I can choose whether to have it present on each device I use or just rely on a cloud connection. Evernote mobile apps can do that. But Evernote Windows desktop could not (though that might have changed). And also why pay twice for cloud storage?
But I'm happy we each find the solution that works for us. I just get e-mails about this thread (because I answered this thread last year saying I'd really like a solution to this, but none sadly came*), so thought it worth mentioning another system for people who ran into the same problem as the thread author, and me.
Michael
*P.S. When I answered last year I said I was thinking of moving to OneNote. I tried it, and it was nice (it's been quietly getting better over the years it seems), but I realised I didn't want to tie myself to another proprietary system, especially as I was starting use use Linux more (OneNote is not supported at all in Linux, whereas Evernote does at least have a community-developed front end, NixNote, which is pretty decent). That's when I went hunting for a simply cross-platform system and found the Free and Open Source TagSpaces.