When you created a lisp machine, it was a lisp machine - everyone knew why and how you did it (to some extent). If you wanted to run it, you ported "the program" to it and all was good. Right now you have users expecting at least the stuff they can get from other popular systems - and that's years of work away for any new project.

The best you can probably do, as far as "progress" goes is to create a new research system and port the good stuff back to mainstream (singularity, plan9, etc.)

To some extent we know all there is to know right now... New languages, periferials, usage ideas are still created. But for a new system language you need to either create or port a system and gather some followers. That's a big step.

Edit: Actually I believe that there's a new hardware change coming that will make current computers ineffective in some way. We could switch to new hardware, new languages, new systems... we could start from scratch :) I don't believe the current ways of parallelising computation can do that.. but if someone constructs a concurrent bus/memory/cpu that could invalidate some of the normal programming ideas.

See, even though Joe Blow may use Windows, he still uses Linux when he Googles. The web allows people to not have to worry about what OS the servers are running... so I think there's lots of room for innovation on the OS front, but on the server side of the cloud.