Here are the things about EverNote that I find problematic:
1. Tags and notebooks
You click on a notebook in the side panel, and you have "opened" that notebook. If you do a search, the results are restricted to that notebook. Good. And if you search for "tag:MyTag", again the results are restricted to the notebook.
But now say I want to do the same thing but utilizing the tag list on the left panel.The first problem is that all the tags are shown, even tags that only occur in other notebooks. Argh. Why is that? Well ok, so I click on MyTag, And all of a sudden, the results are no longer restricted to the notebook that I was using! In fact, at the top of the screen where it showed the name of the notebook that I was in, it suddenly says "All Notebooks".
2. Tag hierarchy in iOS
I read a post by Ian Small that said consistency across platforms is a goal. I hope this means showing the tag hierarchy in iOS. Why is the tag hierarchy shown in Windows, but not iOS?
I have seen comments from within Evernote that tags are unimportant, but I disagree. Search is one aspect of information management, but metadata about how notes are organized and how they relate to each other is information in itself, and that's where tags come in.
I saw one comment where someone suggested that part of the reason why you shoudn't use tags is that the hierarchy isn't shown in iOS!
3. Windows UI
The Windows UI is about the most visually unappealing of any modern application that I have seen.