Could you break down a bit what is bothering you about why prefixes aren't a suitable replacement for subforums?
Absolutely.
While it's true that the new structure will feel more natural once we get used to it, the previous one was "an extra step" into organization.
An example case: Finding the guide to hack your console for the first time. Entering the hacks subforum was the first step, then filtering by guides (in this particular case, that one had a stick).
Now, filtering by guides will bring
all the guides, which leads to longer search times cause now all the information about guides is at the exact same level of hierarchy, regardless if it's the key tutorial to start hacking your console from the scratch of it's how to add more coins to X game.
If possible, I think a potential solution would be to filter by multiple terms. Example: If I click Tutorial, that brings all the Tutorial threads, but then I click ROM Hack and that cleans the filter and brings only the ROM Hack prefix.
If, in this case, that sequence could lead to the ROM Hack threads that are
also part of Tutorial, I think that would solve basically every problem about this particular "issue".
I know the Filters menu do this already, but this way would be more intuiteve, specially for those who are getting used to the forum. And even among veterans, I'm sure most of them don't know about that.
Also, some folks (like me) are kinda dumb, and, at a glance, seeing (for example) three tags with the same red, three with the same cerulean and two with the same orange can lead to confusion. And now that tags are more important since we are sorting the forum using them, maybe thinking of a different color for each one could help as well.