The necessary decarbonization efforts in energy sectors entail integrating flexible assets and increased levels of uncertainty for the planning and operation of power systems. To cope with this in a cost-effective manner, transmission expansion planning (TEP) models need to incorporate progressively more details to represent potential long-term system developments and the operation of power grids with intermittent renewable generation. However, the increased modeling complexities of TEP exercises can easily lead to computationally intractable optimization problems. Currently, most techniques that address computational intractability alter the original problem, thus neglecting critical modeling aspects or affecting the structure of the optimal solution. In this paper, we propose an alternative approach to significantly alleviate the computational burden of large-scale TEP problems. Our approach integrates machine learning (ML) with the well-established Benders decomposition to manage the problem size while preserving solution quality. The proposed ML-enhanced Multicut Benders Decomposition algorithm improves computational efficiency by identifying effective and ineffective optimality cuts via supervised learning techniques. We illustrate the benefits of the proposed methodology by solving multi-stage TEP problems of different sizes based on the IEEE24 and IEEE118 test systems, while also considering energy storage investment options..