Trajectory-based approaches to excited-state, nonadiabatic dynamics are promising simulation techniques to describe the response of complex molecular systems upon photo-excitation. They provide an approximate description of the coupled quantum dynamics of electrons and nuclei trying to access systems of growing complexity. The central question in the design of those approximations is a proper accounting of the coupling electron-nuclei and of the quantum features of the problem. In this paper, we approach the problem in the framework of the exact factorization of the electron-nuclear wavefunction, re-deriving and improving the coupled-trajectory mixed quantum-classical (CT-MQC) algorithm recently developed to solve the exact-factorization equations. In particular, a procedure to include quantum nuclear effects in CT-MQC is derived, and tested on a model system in different regimes.