Both have their limitations:
Molecular Orbital theory is a very good tool in explaining many of the molecular properties, though it too has certain lilmitations: 1. Molecular Orbital theory is based on quantum mechanical principles and hence hard to conceive, especially for the beginners. 2. It does not give any idea of molecular geometry, shape etc. 3. Although it can successfully describe many a properties, explanation of all the molecular properties or bonds is beyond its ambit. A combination of VBT and MOT is required for a more complete understanding. 4. It becomes exceedingly cumbersome, if not impossible, to explain bonding in polyatomic molecules on the light of MOT alone.