As a premium paying customer, I do have to say it's a bit ridiculous how long it is taking them to fix this problem. I've been a paying customer for years, and in general I've been happy to do so. I know the extension has been updated with new features, yet the smart filing has still not been addressed. Very disappointing.
I live in a MS Office world, and of course One Note would be the obvious alternative. However, it doesn't do everything Evernote does which is why I have never switched over. That and I currently have 8,183 notes I don't want to haphazardly 'convert' or lose.