Stop making duplicate bins when importing sequences. Merge them.
When bringing in a sequence from another project (dragging the clip from one project pane to another), Premiere adds all the needed new clips in their bins, but it adds the bins even if my new project already had the same bins. So I end up with two Audio bins, two Footage bins, two Edit bins etc, often with their own sub bins.
If I already have a bin with the same name, the footage should go in the existing bin rather than making a new one.
"Not every user wants to 'just merge everything', but it'd make a nice preference..."
I disagree. It's not uncommon to be working between multiple premiere projects, especially for larger jobs with lots of assets, or for old client work when you're essentially creating a new piece that may rely on some key assets from an old piece.
You don't import everything in one go -- you import a few files, then a few more, then a few more. Every time Premiere creates identical duplicate bins with sub-bins and sub-bins so if it's three layers deep it isn't simple to clean up. It's easy to end up with a dozen duplicate folders in your main project window which does nothing to help you sort through your files.
So you either :
A) Sigh and accept that your nice, neat hierarchies are gone forever
B) Sigh and accept that you will spend far too much time manually pulling things out of bins and relocating them.
Premiere should be smart enough to go "Oh, this is the third time assets have been pulled from that project, I'll put the new assets in the appropriate bins"
NOT insist on turning your project into a basket case.
Not every user wants to 'just merge everything', but it'd make a nice preference...