Are you talking about the same Mac OS 6 and Mac OS 7 that I remember?
Mac OS 6 was good, as you say. But 'System 7' as they called it, was a huge improvement.
* MultiFinder only (no more single-finder)
* Aliases (eg, file system links to folders or files like symlink)
* Organized subfolders within System Folder to fix the clutter. Seperate subfolders for Startup Items, Desk Accessories, Fonts, etc.
* The Apple Menu folder. You could now customize the Apple menu. What items appeared in the Apple menu was dictated by the Apple Menu folder within the System folder. You could now put more than DA's in the Apple menu. You could put apps there. Or aliases to apps or other folders or frequently opened files. Oh, and nevermind that putting a real folders in the Apple Menu made it into a hierarchical menu. This added tremendous flexibility, customizability and convenience to the Mac.
* Fonts as separate files instead of resources within the System file. No more Font/DA Mover.
* DAs as separate files within the Apple menu. No more Font/DA Mover.
* An invisible temp folder where applications could create active temp files. If the app crashed, these moved into the trash can as recoverable files. The most notable example was Microsoft Word (on Mac). If it crashed, of if the entire system crashed, your unsaved changed file could be found in the trash can and simply dragged out.
I'm sure I'm leaving out some things. But those are the ones I remember best from twenty plus years ago.
System 7 was a gigantic step forward for the classic Mac OS. System 8 and 9 not so much. System 8 had a few improvements, like dockable folders that could appear as tabs at the bottom of the screen. System 9 had no visible improvements. Then by that time classic Mac OS was beginning to stagnate by the late 1990's, Apple was fumbling with their new OS, and it was beginning to be obvious.