A. Neumaier said:
No. Using vectors, matrices and functions is the natural way of describing any (mathematical or physical) system with a large number of degrees of freedom. For example, nonlinear manifolds are represented in terms of vectors when doing actual computations.
The classical phase space for a particle in an external field is also a vector space ##R^6## (or ##C^3## if you combine position and momentum to a complex position ##z=q+i\kappa p## with a suitable constant ##\kappa##). And, unlike in the quantum case, one can form linear combinations of classical states.
Thus the problem with quantum mechnaics cannot lie in the use of vectors and their linear combinations. In the quantum case you just have many more states than classically, which is no surprise since it describes systems form a more microscopic (i.e., much more detailed) point of view.
What one must get used to is not the superpositions but the meaning attached to a pure quantum state, since this meaning has no classical analogue.
However, for mixed states (and almost all states in Nature are mixed when properly modeled), quantum mechanics is very similar to classical mechanics in all respects, as you could see from my book. (Note that the math in my book is no more difficult than the math you know already, but the intuition conveyed with it is quite different from what you can get from a textbook.)
Thus the difficulty is not intrinsic to quantum mechanics. It is created artificially by following the historically earlier road of Schroedinger rather than the later statistical road of von Neumann.