Like most critics of the molecular manufacturing concept, Jones is attacking a straw man. Yes, Drexler’s initial vision of how to design nano-scale machines was a bit naïve, but we’ve known that since the 1990s and no one is claiming otherwise. The fact that mechanical engineering at the nano scale is different than at the macro scale should surprise no one, but different does not mean impossible (or even more difficult, really). See, for example, the extensive work of Robert Freitas analyzing the actual challenges and opportunities of nano-scale medical engineering.
What are the plausible scientific limits of molecular nanotechnology?
Richard Jones, author of Soft Machines has written an interesting critique of the room-temperature molecular nanomachinery propounded by Drexler:
Rupturing The Nanotech Rapture
The entire article is definitely worth a read. Jones advocates more attention to "soft" nanotech, which is nanomachinery with similar design principles to biology -- the biomimetic approach -- as the most plausible means of making progress in nanotech.
As far as near-term room-temperature innovations, he seems to make a compelling case. However the claim that "If ... such devices can function only at low temperatures and in a vacuum, their impact and economic importance would be virtually nil" strikes me as questionable. It seems to me that atomic-precision nanotech could be used to create hard vacuums and more perfectly reflective surfaces, and hence bring the costs of cryogenics down considerably. Desktop factories using these conditions could still be feasible.
Furthermore, it bears mentioning that cryonics patients could still benefit from molecular machinery subject to such limitations, even if the machinery is not functional at anything remotely close to human body temperature. The necessity of a complete cellular-level rebuild is not a good excuse not to cryopreserve. As long as this kind of rebuild technology is physically plausible, there arguably remains an ethical imperative to cryopreserve patients facing the imminent prospect of decay.
In fact, this proposed limitation could hint at an alternative use for cryosuspension that is entirely separate from its present role as an ambulance to the future. It could perhaps turn out that there are forms of cellular surgery and repair which are only feasible at those temperatures, which are nonetheless necessary to combat aging and its complications. The people of the future might actually need to undergo routine periods of cryogenic nanosurgery in order to achieve robust rejuvenation. This would be a more pleasant prospect than cryonics in that it would be a proven technology at that point; and most likely the vitrification process could be improved sufficiently via soft nanotech to reduce the damage from cooling itself significantly.