I think we have actually made progress with HTTP and all the REST. But I feel that the great failure of distributed object systems in the 1990s and 2000s has left a great void when it comes to new thinking about more fine grained sort of interfaces between programs.
Functional programming has influenced so many things but hasn't really arrived in the systems corner of the world yet. Also, looking at the sort of query capabilities of online streaming databases and complex event processing systems I get the feeling that there may be a lot of potential in combining that with Unix pipes and text streams.
Publish-subscribe ala zeromq is also something that could be a core part of modern Unix.
Sorry about the half-baked mess I'm dumping on you here :)