The main feature of QM is not its discreteness. The discreteness of some quantities like energy levels in atoms is a secondary aspect particular to some quantum systems. The analogy here is like a violin string, which is continuous, yet has discrete harmonics due to its being tied down at both ends.
However, one can largely imagine that the matter we see is made from a discrete lattice, where the lattice spacing is fine enough so that we cannot see it with current experiments. There is one difficulty with this view, which is whether chiral interactions can be put on the lattice, which I think is still being researched. You can read more about this point of view in
http://www.staff.science.uu.nl/~hooft101/lectures/basisqft.pdf:
"Often, authors forget to mention the first, very important, step in this logical procedure: replace the classical field theory one wishes to quantize by a strictly finite theory. Assuming that physical structures smaller than a certain size will not be important for our considerations, we replace the continuum of three-dimensional space by a discrete but dense lattice of points. ...
If this lattice is sufficiently dense, the solutions we are interested in will hardly depend on the details of this lattice, and so, the classical system will resume Lorentz invariance and the speed of light will be the practical limit for the velocity of perturbances. If necessary, we can also impose periodic boundary conditions in 3-space, and in that case our system is completely finite. Finite systems of this sort allow for 'quantization' in the old-fashioned sense: replace the Poisson brackets by commutators. Note that we did not (yet) discretize time ..."
At the end of that article, 't Hooft discusses taking the lattice spacing to zero, which at the moment cannot be done, because of the "Landau pole" of QED. He then says the problem is probably not so important on its own, because the Landau pole is above the Planck scale, and one would presumable need to solve the problem of quantum gravity too.