In addition to the probabilistic and particlelike elements of the quantum wave function, we also have the mathematical difference that the QM wave function uses a -i d/dt not a d2/dt2. For wave functions that correspond to particles of definite energy and wave modes of definite frequency, the two work the same (if we deal with complex amplitudes appropriately, according to whichever interpretation we are using), but in the general case (particles with no definite energy, wave modes that superimpose frequencies), these are mathematically different. For one thing, a second-order in time equation requires two initial conditions, often the wave function and its first time derivative at t=0, whereas a first-order in time equation requires only one (often the wave function at t=0). That's a pretty important difference-- classically, we need to know the current state and how it is changing (analogous to position and velocity of the particles), but quantum mechanically, we need only know the current state, and how it is changing in time is prescribed automatically.
Now, since we view quantum mechanics as the more fundamental theory, we would tend to regard it as "closer to the truth" in some sense, so we would tend to think that the universe does not need to be told how it is changing, only what its state is. So then we can ask, not why is QM a d/dt, but rather why is CM a d2/dt2? Why did we think we had to be told the particle velocities and positions, when in fact it is inconsistent to know both at the same time? Apparently it is because our measurements were so imprecise, we could better "pin down the state" by including information about both position and momentum. More precise measurements actually mess with the system in ways that we tend to want to avoid, so we found it is better to combine imprecise measurements and we can still make good predictions in the classical limit without strongly affecting the system.