(please forgive my english. i promise never again to write such a long post 
)
Now i am a subscriber since almost an half year. But i must admit after my first sight into bear i decided to deinstall it because of the lack of so-called folders. The radical approach of organising all notes just by tags was too much for me. A few months later after reading that also bear supports wiki-links to connect notes i gave it a new try. After having discovered that bear automatically sets a certain tag when you create a new note while having chosen that tag in the tag tree from the left side pane, i felt exited not being forced always to set a tag manually by writing it. Therefore tags are better than folders in terms of functionality
In the meantime i like the approach of bear but nevertheless there are some inconveniences and additionally to them mainly the way how the tag tree in the left pane is builded makes me feel uncomfortable sometimes in special scenarios. There are enough users who requested folders. I fully understand that request but on the other side i also understand the argument that tags are nothing else but folders with the special feature that different folders (tags) can hold the same document.
I spend some thoughts and reflection to see what inconveniences are bothering me and other user. I am going to summarise some of these thoughts in the following points A and B. While point A shows some nuisances and possible solutions in regard to long tag tree in left pane and long nested tags, the point B addresses the main reason why people ask for folders in my eyes. In that regard point B is the more important one. So let’s start!
A. Shortening tag tree and nested tags
The more notes you collect the bigger the tag tree in the left pane becomes. At some point you get a huge and unmanageable list of tags that is just sorted alphabetically.
1) Workspaces
As far as i can see workspaces are not quite unpopular. There are several requests here in the forum. It is evident how workspaces are able to drastically shorten the tag tree and how to offer a better overview. Why mixing notes in one view that never will get in touch because they belong to totally different areas? Why mixing private stuff like travelling or cooking with stuff related to university like chemistry or mathematics? Let’s say the average user will create 4 workspaces - that means that the length of the tag tree in left pane in average will be reduced to 25% which is a huge success in cleaning up.
While workspaces would reduce the length of the tag tree the following subpoint shows how the length of the nested tags could be reduced:
2) Linking each tag to everyone else
Preliminary consideration
Let’s say you have a tag like #recipe/ingridients/vegetable/broccoli. Wouldn’t it be better to choose two tags rather than that one? For example: #recipe and #vegetable/broccoli? For sure the handling and writing of tags would be better but the linking between recipes and ingredients will get lost: we can choose recipes in the tag tree but we have not anymore access to the ingredients. So we are forced to keep the long tag with 4 levels to have that connection.
That leads furthermore to the necessity to accept the repeated appearance of the same subtag in several nested tags. Here an example:
You love New York City and are collecting notes from that town with different topics: #travel/city/new_york and #sports/city/new_york. It would be useful to split up these into several shorter tags: #travel , #sports and #city/new_york. So the combination „city/new york“ will appear just one time in the tag tree. But also here the same problem: we will loose the linking between the tags.
Last but not least: Even if you don’t care about what i have written above and you like to write nested tags with even 6 levels, you always will missing desired connections. Here an example: #recipe/ingridients/vegetable/broccoli , #recipe/type/vegetarian or #recipe/country/italian. Everything is linked to recipe, but you have not a linking to „countrys“ or to „type“ once you choose „ingredients“.
To sum it up:
We are not able to create tags along logical categories like topic, place, time, attributes, rating and so on but we are forced to consider what we wish to be linked together while furthermore one linking of a tag to another makes it impossible to link it to a third tag at the same time.
Solution
So what we would need is a feature that is able to link each tag to anyone else. And i think i have an idea which is on one side able to realise that but on the other side is still intuitive and would not disturb aesthetically and minimal approach of bear. The idea is about a search feature inside the second pane where the notes are listed. That search feature is even more than just about shortening tags or splitting them up in logical categories. It is extremely useful for searching notes and i have not found it in any note app although it is actually simple and obvious.
Ok, here comes the proposed feature! Let’s say you choose #recipe in the left pane what results in an huge list of notes. Just imagine besides the search bar of the second pane resides an icon like that:
And that icon opens a popup which shows all remaining tags founded in the note list. See the mock-up below to get what i mean:
(Ideally the checkboxes in the pop up would have three states: empty, include, exclude)
With the help of the checkboxes you can choose by which further tags you want to filter the notes list. Even multiple choices are allowed whereby a multiple selection of more than one tag mean that they are connected by a logical „OR“. But here the feature doesn’t end. Once the note list is filtered by that feature you can reopen the pop up again and will get a further shrinked list of the remaining tags. In other words: In the first cycle i filter my recipes by country and in the second cycle i filter it by ingredients. the choices between two or more cycles are connected by a logical „AND“. And to show the active filters something like that below could be placed under the search bar:
I hope you get the idea: By one simple pop up menu that resides beside of the searchbar and that shows JUST the tags from the listed notes in the second pane, you could link each tag and subtag to anyother else. That influences the strategy how and what tags to create. Benefits are: shorter tags and a more logical structure of nested tags. Actually that feature offers something like a database view with simple means
B. Manual construction of the tag tree from the left side pane itself
Take a look into the app „UpNote“. It has tags like bear and it has folders that do not exist in bear. Furthermore „UpNote“ offers the feature that the same note can be placed in more than one folder. That ends in the strangeness that there is no difference between tags and folders in terms of functionality. So what is the real reason people are asking for folders. Actually it is quite trivial and evident: it is not the functionality but HOW the folder structure is builded up.
In the logic of building up folders you FIRSTLY create the folder structure and THEN you place the notes in them. In the logic of building up a tag structure you in opposite FIRSTLY create the note and THEN by adding more and more tags you build up gradually and slowly the tag structure. And that is exactly the point why tag structure sometimes are unattractive and tedious.
So far as i can see there are two ways in bear to set tag: either manually inside the note or by creating a new note while a certain tag is chosen in the left pane. I would advocate for a further way and for the feature to create tags manually (means by context menu) in the left pane: „add tag“ and „add sub tag“. It is not just a bad habit to crate an organisational structure like that but indeed a big relief. In some cases it is ok when the tag structure grows with each tag you write inside a note. But often enough it is a great help to finish the building of the organisational structure BEFORE starting to add notes to it.
One serious point remains: To make that solution possible empty tags have to be accepted, means: the tag tree would show tags or subtags that are not written in any note. But i must say that i even would like that for other reasons too, f.e. after removing a certain tag from all notes it still remains in the popping up list after starting to write a tag.
The only added complexity i see is that it is necessary to differentiate between „removing“ a tag (removing it from all notes) and „deleting“ it (removing it completely from left pane). But i think that price is worth it. Last but not least: Empty tags could be displayed a little bit paled out to show that they are empty
C. Last remarks
I like the radical approach to let tags do the most organisational work. Nevertheless, it is not a good idea to let them do 100% of organisation, 99% would be better 
What i am thinking about? F.e favourite notes! Yes, i can add it as a tag, BUT it is a toggle off and on attribute. Therefore setting or unsetting a note as favourite should just be a matter of one and only click