I think the only thing wrong with the Amiga is simply the lack of money being thrown at it, little developement compared to Windows. It's still a hell of an OS though, a very solid foundation that a lot can be built on. It's very efficient, very flexible, and fairly simple. It was built back when computers were actually fun and did what you wanted instead of what they want. Everytime I try and do something I spend a lot of time trying to figure out how to get around Windows because it stops me on everything I try. The Amiga just lets me do it.
With the Amiga I can simply copy all the files from a running OS, you don't have to use a special backup program. If I want to move a program to another directory or a flash drive I can with little effort to get it running again. The list just goes on and on, the Amiga is just way less convoluted and much more flexible and I can pretty much do what I want.
The way I invision the Amiga OS and Windows is like this. The Amiga is a very large, very strong, steel reenforced concrete foundation with a little shack sitting in the middle of it. Windows is the Sears tower sitting on a very weak crumbling foundation and they have to use many guy wires to keep it from falling over.
Now don't get me wrong, because of the money being spend on Windows, it's generally much more powerfull then the Amiga, but the Amiga is much more fun. I just write the programs I need which is also fun.
As far as protected memory goes, I feel that's a disadvantage. It just makes it easier for stupid bugs to hide and eventually raise their ugly heads. Running Enforcer and Mungwall while developing on the Amiga, it's pretty difficult to have stupid bugs. Back in the days when everybody was logged onto main frames and writing and testing programs, it was necessary. Now days the worst case would be servers, but even with servers people log onto the server program not the OS, you can only do what the server program lets you do. If the server program is bug free then no problems. Considering how many times I've had problems with servers over the years I'd say there's quite a few bugs hidding in them. The bugs are protected.