Massive multiple-input multiple-output (MIMO) systems use antenna arrays with a large number of antenna elements to serve many different users simultaneously. The large number of antennas in the system makes, however, the channel state information (CSI) acquisition strategy design critical and particularly challenging. Interestingly, in the context of massive MIMO systems, channels exhibit a large degree of spatial correlation which results in strongly rank-deficient spatial covariance matrices at the base station (BS). With the final objective of analyzing the benefits of covariance-aided uplink multi-user CSI acquisition in massive MIMO systems, here we compare the channel estimation mean-square error (MSE) for (i) conventional CSI acquisition, which does not assume any knowledge on the user spatial covariance matrices and uses orthogonal pilot sequences; and (ii) covariance-aided CSI acquisition, which exploits the individual covariance matrices for channel estimation and enables the use of non-orthogonal pilot sequences. We apply a large-system analysis to the latter case, for which new asymptotic MSE expressions are established under various assumptions on the distributions of the pilot sequences and on the covariance matrices. We link these expressions to those describing the estimation MSE of conventional CSI acquisition with orthogonal pilot sequences of some equivalent length. This analysis provides insights on how much training overhead can be reduced with respect to the conventional strategy when a covariance-aided approach is adopted.