I don't know where to start, so forgive me, but I am going to ramble.
MNT is going to happen. It's a matter of time. Not if, but when. For it to be successful and useful, there are going to have to be some very significant advances in several sorts of fields. Some of them are advancing by leaps and bounds already, but there is plenty of room to grow.
Chemistry. Synthetic chemistry cannot currently create the kinds of things needed to make MNT feasible. It may be that it will used to create the first gen of it and then bootstrap from there. Computational chemistry, the quantum side in particular, must also be advanced a great deal. Unless there have been major advancements over the last 8 years that I am unaware of, the level of precision in computing chemical structures is prohibitively computationally expensive - the magnitude of error tends to be on the order of the strength of a chemical bond, which while it is very close in absolute terms, it renders the computation almost useless.
Algorithms in math and computer science. Serious improvements in algorithms could greatly reduce the time required for predicting chemical structures. My own PhD work represented a good advancement in optimization of functions, but that does not decrease the time required to compute the energy of a single structure.
Parallel computation. The use of this is twofold. Parallel computers are really starting to take hold in mainstream systems, and properly using them would greatly enhance the speed of predicting structures. Later on down the road, fault tolerant systems will be needed to handle truly massive parallel architectures - imagine a personal computer with trillions of processors and you're starting to get the picture. Processors would be continuously added and removed from the system, error checking and redundancy would be needed, and so on.
Programming languages. Again, parallelization. There are advancements being made in this arena to handle multiple processors, but I have no idea if they handle dynamic addition and removal of cores, along with fault tolerance. Such a language must be easy to use or people will not be able to adequately deal with the scope of the problems to be dealt with.
Artificial intelligence. In particular, the ability to partition problems and solve subproblems. This goes back to parallelization and programming, among other things.
Encryption and security. The homegrown encryption routines used by corporations in their efforts to enforce DRM are woefully inadequate, and there must be active safety protocols in place from the very beginning. A small imbalance of power, a minor error, or a deliberate attack or sabotage could yield a catastrophe beyond anything seen before. Additionally, there must be a way to enforce end user rights as well, or people will be left with no ability to be self sufficient and/or choose to opt out of this system.
Database technology. I do not know the limitations of current database systems, but I suspect they will be far from adequate for the volume of data coming down the pipeline for projects involving MNT designs. Even breaking down systems into a fractal-like heirarchy, there are still vast numbers of atoms to be accounted for in even the simplest of MNT systems, along with the instruction set coded for the assembly of the system in question.
Intellectual property and economic theory. This ties into encryption and security. Energy, rare elements, structural designs, and items of sentimental value will be the only things of monetary value - in fact, one could argue that that's true today, as well. The most useful elements for MNT are typically going to be the ones most commonly found on the planet - carbon, silicon, nitrogen, oxygen, hydrogen. Trace elements will be useful as limiting reagents. There will almost certainly be certain "open source" designs that will be carefully evaluated as safe for general use.
This is just the tip of the iceberg. All of these things have been thought of before by people involved in MNT, and are just what I can think of off the top of my head. Each and every one of these represents a potential business opportunity with profits to be made along every step of the way, not just after the fruition of MNT.
And I don't know where to start. I just know I am once again really starting to get the itch to walk down this path once more.