There are not only consumers which want to download ebooks with ads. There could be an area of innovative and experimental use where Universities want to develop novel applications - applications that might be written in Smalltalk, Lisp, Haskell - or any other language that can compile and is not Objective C. In many cases the innovation lies in the core logic and the innovative use of a touch screen. Why should I develop my core logic in a way that it is tied to the iPhone or iPad (assuming that the iPad will get the same developer agreement) and where I have to use a relatively low-level language like Objective C.

It is one thing what you assume Apple's target (Adobe, cross platform frameworks, ...) is and another thing who else is also affected by these clauses the developers have to agree to.