Why not just run the old apps in an emulator box so that each CMT app thinks that it's the only application running on its own, with its own copy of RISC OS? This might mean that each application has an additional 4meg overhead or so. The real work would be making it seamless but it should be possible with an OS like RO and some patches to the window manager. I never understand this obsession with maintaining full binary and source compatibility with old hardware and OS. For example, Amiga OS has stuck to this and it's now pretty much an unsellable proposition due to the lack of memory protection. All to run ancient software that can be emulated at a faster speed than the original hardware anyway. Would RISC OS devs mind if there were a few new calls added to the system in order to run as a full pre-emtive app? Maybe someone who has done more WIMP programming than me (I was mainly a asm game and demos kind of guy) could tell us how big the changes would have to be.
Secondly, couldn't someone make an RM for handling the second core as a co processor? All programmers need is an interface instruct the second core to run a piece of code at a certain address and deposit the result at another address. That seems like a far more realistic goal than reinventing RO as a truly multi-core operating system.