The upgrade to the National Spherical Torus eXperiment (NSTX-U) included two main improvements: a larger center-stack, enabling higher toroidal field and longer pulse duration, and the addition of three new tangentially aimed neutral beam sources, which increase available heating and current drive, and allow for flexibility in shaping power, torque, current, and particle deposition profiles. To best use these new capabilities and meet the high-performance operational goals of NSTX-U, major upgrades to the NSTX-U control system (NCS) hardware and software have been made. Several control algorithms, including those used for real-time equilibrium reconstruction and shape control, have been upgraded to improve and extend plasma control capabilities. As part of the commissioning phase of first plasma operations, the shape control system was tuned to control the boundary in both inner-wall limited and diverted discharges. It has been used to accurately track the requested evolution of the boundary (including the size of the inner gap between the plasma and central solenoid, which is a challenge for the ST configuration), X-point locations, and strike point locations, enabling repeatable discharge evolutions for scenario development and diagnostic commissioning.