Some more reasons:
Bond energies are big, but reactions break some to create others, and the difference is usually much smaller, so any tiny inaccuracy in bond energies has big consequences on a reaction enthalpy.
In some compounds, cyclic or cage molecules, aromatics and resonances, bond energies apply very badly, because the angles or distances are forced or for other reasons.
Bond energies use to neglect whether the compound is gaseous, liquid or solid, but in a reaction enthalpy it's quite visible. As well, molecules store heat as rotations, vibrations... that bond energies don't estimate properly. Software estimates of individual molecules have the same bad limit.