Although the specific area of molecular electronics (meaning molecular transistors) is vastly overhyped (and the Wired article doesn't help), I still think there are incredible opportunities out there if we are able to harness the electronic (meaning in this case, relating to electrons) properties of molecular-scale systems. Examples could include designing our own catalysts, pharmaceutical molecules, light-harvesting systems, or industrial materials from scratch. Limiting the search for applications of these systems to the traditional three-terminal electronic switching device, while making the subject easier for laypeople to relate to, does a disservice to a whole spectrum of other exciting other options.
Having dealt with carbon nanotubes as part of my M.Sc. thesis, I miss a comment on that and another major obstacle: can we properly manipulate and align these components to structure circuits? We are still a long way from that with nanotubes.
As for real circuit fabrication, you are absolutely right; I would even go so far as to say that placing these individual molecules in some kind of circuit topology is an order of magnitude harder than doing the same with CNTs. I don't think they've even started working seriously on that problem yet, and I wouldn't, either; you have to be able to make reasonable amounts of working devices first...
That was the first thing that jumped out at me. What's the point, then? The article doesn't say.
In traditional (solid-state-based) transistors, smaller dimensions has always meant faster switching speed, less energy waste and more efficient use of chip real estate. I fail to see how any of these are applicable to molecular-scale devices, although I could be wrong.
I think the proper way to see this is as a feat not of engineering, but of experimental physics; in that light, the mere novelty of having fabricated a single-molecule switching device has plenty of merit on its own. For real engineering applications, as I mentioned in the parent post, this specific example is probably of limited use, but could help pave the way for the development of other designed molecular systems.
Also, I'm afraid there is pr value in claiming to have created the ultimate incarnation of Moore's law, regardless of any actual engineering applicability. This could also have provided some of the incentive for this work.
