TL;DR
VB theory treats atomic orbitals (including hybridized orbitals) as providing a good mathematical/physical description of the true form of the molecular wavefunction. MO theory uses atomic orbitals (with Gaussian radial functions) as a tool of computational convenience in an effort to define a molecular wavefunction that in its final form often bears little resemblance to the original atomic orbitals, or to the VB theory description.
Long Version
The key difference between the VB and MO theories lies in their respective assumptions of the underlying mathematical/physical form of the electronic wavefunction.
VB theory holds tightly to the mathematical structure of atomic orbitals (AOs), assuming that the electronic structure of a molecular system is described adequately by retaining the atomic orbitals (possibly hybridized) from each constituent atom, and overlapping them to form the needed description of bonding. VB calculations are computationally much more complex: the AO basis is generally non-orthogonal, and the linear algebra and other techniques required to cope with this non-orthogonality are much more involved.
More broadly, the need to invoke resonance (superposition of multiple valence-bond structures) and other concepts highlights that, in fact, often this adherence to atomic orbitals and their valence-bond overlaps is not adequate for a proper description, at least not without extensive use of methods analogous to the configuration interaction of MO theory. VB theory does hold certain advantages, however—for example, I believe the AO basis does sometimes allow for a more direct linkage to fundamental chemical concepts such as hybridization and Lewis electon-pair theory. To note, Sason Shaik is one of the strongest modern proponents of the theory I know of—he describes some of these strengths and their applications in his recent retrospective article (doi:10.1016/j.comptc.2017.02.011).
MO theory, at its core, casts away most assumptions regarding the mathematical structure of the electronic wavefunction, as long as properties like indistinguishability and the Pauli exclusion principle remain satisfied. Calculations within MO theory can use a wide variety of mathematical structures to try to represent the wavefunction, ranging from gridded numerical quadrature approaches (see here and here, and also orbital-free DFT) to Slater orbital computations to the Gaussian-orbital based calculations used most commonly today.
One potential point of confusion is that MO theory in its most common implementations makes direct use of atomic orbitals in composing the molecular wavefunction (see LCAO theory). The distinction to be made here is that instead of attributing significance to the atomic orbitals as an intrinsically good descriptor of electronic structure, they are used merely because they afford a convenient mathematical form for efficient computation, in trying to construct the MOs. Particular advantages are obtained from the use of atomic orbitals constructed from Gaussian functions, since the product of two Gaussians is another Gaussian (even in multiple dimensions) and numerical integration of n-dimensional Gaussian functions is straightforward.
It should be noted that, for as much of an improved description it affords, MO theory still is an approximation. For a given system, the electronic wavefunction just IS the highly-abstract mathematical object that satisfies the appropriate Schrodinger equation. MO theory is used extensively because it provides one of the most computationally tractable paths to getting in the neighborhood of the "real answer."
Practical Aspects of MO theory
The "simplest version" of MO theory for a time-independent system under the Born-Oppenheimer Approximation is the Hartree-Fock method, which provides a remarkably good description considering the significant simplification represented by its mean-field approximation of the electron-electron interactions. Hartree-Fock is in general not good enough for computations at the level of chemical accuracy (~$1\mathrm{\ kcal/mol}$), however, and numerous methods have been developed to refine it: the most often used techniques are Moller-Plesset perturbation theory, configuration interaction, and coupled cluster.
In-Depth Reading on MO Theory
For a deep dive into the underlying mathematics of MO computations, it's hard to beat the classic Szabo & Ostlund. As a more readable, lighter-weight introduction to MO theory and its implementations, I would recommend Frank Jensen's Introduction to Computational Chemistry.