This paper proposes a flexible pilot assignment method to jointly optimize the uplink and downlink data transmission in multi-cell Massive multiple input multiple output (MIMO) systems with correlated Rayleigh fading channels. By utilizing a closed-form expression of the ergodic spectral efficiency (SE) achieved with maximum ratio processing, we formulate an optimization problem for maximizing the minimum weighted sum of the uplink and downlink SEs subject to the transmit powers and pilot assignment sets. This combinatiorial optimization problem is solved by two sequential algorithms: a heuristic pilot assignment is first proposed to obtain a good pilot reuse set and the data power control is then implemented. Numerical results manifest that the proposed algorithm converges fast to a better minimum sum SE per user than the algorithms in previous works.