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)
So because they took out the stable, single-tasking finder system and only made the unstable multifinder available, that's good? Understanding Apple, you fail it. Apple has told you all along that if they didn't have it, you didn't need it. Then it comes along in a later machine or release.
* Aliases (eg, file system links to folders or files like symlink)
Yeah, the problem with Aliases was that they only worked about half the time. Half the time an application tries to open the Alias as a file, the other half it tries to open the file the Alias points to. Half the early applications would see a folder alias as a folder, half of them would totally fail to comprehend it.
Organized subfolders within System Folder to fix the clutter
Totally irrelevant because System 6 let you sort by type, and because anyone who had enough fonts to go in there regularly had a font manager.
* Fonts as separate files instead of resources within the System file. No more Font/DA Mover.
Totally irrelevant because anyone who diddled fonts regularly used a font manager. Same answer for your "next" point, which is really the same point.
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).
Please listen to yourself. In actuality, applications could always do this -- without hiding the files in some inscrutable temp folder. And they did. In fact, Word was one of these applications. I have an accelerated SE with Word 5.1. Sometimes I use it as a doorstop.
System 7 was a gigantic step forward for the classic Mac OS.
That was what I thought, until I used it regularly.