I agree with the four items listed in "Problems with Today's Desktop Environments and Applications". However, these are not the only issues. (I even thing the older Windows 3.1 and even older UI were well enough; you don't need such fancy graphics.)
Your "Monolithic Applications versus Composable Tools" also is reasonable. What you list about Unix philsophy are the good ideas of Unix philsophy; it is too bad that many modern programs don't support it. I would allow command-line and GUI and easily interact between them.
My idea involves capability-based security with proxy capabilities, and a program can send/receive/wait with capabilities it has access to; a message send/received consists of bytes and/or capabilities. (It is also similar than actor model in some ways.) This is what the kernel does (and programs can create their own capabilities called "proxy capabilities"); all I/O is required to use capabilities. (When a program starts, it must receive an initial message containing some capabilities, so that it can do I/O.)
My idea also is to make the format which will be called "Common Data Format"; it can store documents, databases, and other stuff, and can be used in command-line and GUI. (It also involves some of the ideas of OpenDoc, and of TRON Application Databus, but is different from both of them.)
There are also many other considerations: hypertext file system, window indicators, security, TRON character code, network transparency, emulation, etc.
About "Not a New Operating System", my idea would be that the specification can be done and implementations of the individual parts can be done independently and interchangeable, and that an implementation can be made to run stand-alone or inside of another operating system (something that Inferno also does); this can avoid the problems of drivers at first, while when it is made stand-alone, drivers can be made for it in that way, too. However, I do not intend to include a web browser by default.
(For making such a thing on Linux, I don't know exactly what capsicum blocks; capabilities are supposed to required for all I/O including accessing the current date/time. My system idea is similar like if you have only socketpair to create new channels of communication, and being able to send/receive messages that may contain SCM_RIGHTS, and the ability to wait for objects.)