Beyond side channels I'm even more worried about the ever present issues of poor security design/architecture and of security-critical components being written in unsafe languages. The fact that there is always another buffer overflow waiting in the kernel, in the browser, etc is nonsense. Who knows when someone will find a critical vulnerability in libjpeg and start manipulating images to take over the browser, then call a vulnerable syscall to install a rootkit.
I really want to run a microkernel (so poorly written driver code doesn't compromise the whole system) written in a safe language with arbitrarily nestable security contexts (eg. beyond users having different privileges, I want any program to be able to spawn processes, threads, etc in more restricted contexts, which can also spawn more restricted children, etc).
Also I want a modern Lisp machine...
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