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Overall a nice review, but I have a couple of quibbles. I can't swear to this, since I haven't yet played around with Jaguar myself, but I think you would have had fewer problems and perhaps better performance if you had done a clean install. That in itself is a black eye for Apple -- an upgrade install shouldn't cause problems -- but if you have the time I would recommend doing a clean install of Jaguar and seeing how that works for you.

I thought one point you made was rather odd: "While it is very easy to unpack applications for Mac, the problem is that there are so many kinds: .bin, .hqx, .sit, .dmg, .tar.gz, .pkg and some others that I can't remember now. Besides the fact that they are too many, the main problem is order." First, this isn't a bug, this is a feature. I can't see how it's a bad thing that many different formats are supported. Second, this has little to do with Apple. It's Stuffit Expander that supports all these formats, and it's individual developers who decide how they want to distribute their application. Maybe all developers should use the installer, but I like the convenience of drag 'n' drop installation.

As to files being unpacked on the Desktop rather than the Applications folder, consider that only .pkg files are specifically installer scripts. .Dmg files are disk images, so of course they mount on the Desktop like ordinary disks. The rest are compressed files that get unpacked wherever they happen to be. It would be absurd for, say, an archive of compressed mp3 files to automatically unpack in the Applications folder. Alternatively, you can select a default destination directory for uncompressed files in the Stuffit Expander preferences.

And as for imposing a structure of subfolders within the Applications folder, the Mac Way has always been to leave organization to the taste of the user. Traditional-minded Mac users already find the OS X file structure too rigid and Unixy. There's nothing stopping the user from creating subfolders, if that's his or her desire, but unless most users are as orderly as you I don't think that should be the default organization.

I've got a solution to one of your problems. You mention, "For example I want to be able to open a terminal on the current directory when I am deep in a Finder directory." Dragging a folder onto the Terminal window will change the shell to that directory. If the folder you want is already open, drag its proxy icon in the Finder window title bar into the Terminal window.