These are mainly things that are better than the Win shell as I have too little experience with the Linux shells to comment on them. And remember these things have been around on OS/2 since 1992. I would hope that some of the Linux shells would have caught up in the last 11 years. :-)
1) Work Areas:
It's a special folder object that remembers the state of its contents. E.g. You can open a Work Area folder, start some Program Refrence objects in that folder. When you're done, you can simply close the WA folder and it'll close the open programs. When you reopen the WA folder, it'll automagically restart the programs that were open when you previously closed the WA.
2) Lots and Lots of customization:
E.g. Each folder can have a different background if you want because each folder is a unique object.
3) Multiple startup folders are possible because the Startup folder is a type of folder, not one that has a special name.
4) It's reasonably simple to backup and transfer your desktop to another machine. You can backup and transfer individual objects to another machine too. You can automate and manipulate the WPS with REXX (the scripting language).
5) Lots and lots of available add-ons to replace/extend the desktop. You can have a Win-like taskbar if you want, or not. You can run OS/2 with the WPS or not.
6) You can move objects between drives and the WPS will automatically keep track of where it was moved to. No brain-damaged broken links like on Windows.
7) It's easy to configure DOS programs to act properly. I still have trouble getting Win32 console-mode programs to come up with the fonts and window size I want when started from the startup folder under Win2k, and there's a text mode DOS program that intermittently hangs under Win2k that's driving me nuts....
8) Drag and drop printing. Drag and drop backups. Lots and lots of D&D functionality.
9) Consistent mouse button actions. Mouse Button 1 (usually the left button) selects an object, MB2 lets you manipulate it. Consistent keyboard shortcuts and a list of them in the Help.
Some drawbacks:
1) It's rather resource hungry so it needs at least 16 MB of RAM. Not much of an issue these days, I know. ;-)
2) It can be rather fragile, but is much more robust than it was in OS/2 2.0.
3) You can't have an animated desktop like you could with OS/2 1.3. :-( E.g. the Deskpic screen saver could have a fish tank with carnivorous fish as your desktop, IIRC. I'm surprised that someone hasn't extended that idea to the more modern OSes.
That's about all I can think of at the moment.
Cheers,
Scott.