This paper considers pilot design to mitigate pilot contamination and provide good service for everyone in multi-cell massive multiple-input-multiple-output systems. Instead of modeling the pilot design as a combinatorial assignment problem, as in prior works, we express the pilot signals using a pilot basis and treat the associated power coefficients as continuous optimization variables. We compute a lower bound on the uplink capacity for Rayleigh fading channels with maximum ratio detection that applies with arbitrary pilot signals. We further formulate the max-min fairness problem under power budget constraints, with the pilot signals and data powers as optimization variables. Because this optimization problem is non-deterministic polynomial-time hard due to signomial constraints, we then propose an algorithm to obtain a local optimum with polynomial complexity. Our framework serves as a benchmark for pilot design in scenarios with either ideal or non-ideal hardware. Numerical results manifest that the proposed optimization algorithms are close to the optimal solution obtained by exhaustive search for different pilot assignments and the new pilot structure and optimization bring large gains over the state-of-the-art suboptimal pilot design.