In this paper, we examine the control of a scramjet-powered hypersonic vehicle with significant aeroelastic- propulsion interactions. Such vehicles are characterized by open loop unstable non-minimum phase dynamics, low frequency aero-elastic modes, significant coupling, and hard constraints (e.g. control surface deflection limits, thrust margin). Within this paper, attention is placed on maintaining acceptable closed loop performance (i.e. tracking of speed and flight path angle commands) while satisfying hard control surface deflection constraints as well as stoichiometrically normalized fuel-equivalency-ratio (FER) margin constraints. Control surface constraints are a consequence of maximum permissible aerodynamic loading. FER margin constraints are a consequence of thermal choking (i.e. unity combustor exit Mach number) and the fact that thrust loss may not be captured for FER greater than unity. Such limits are particularly important since the vehicle is open loop unstable and "saturation" can result in instability. To address these issues, one can design conservative (i.e. less aggressive or lower bandwidth) controllers hat maintain operation below saturation levels for anticipated reference commands (and disturbances). Doing so, however, unnecessarily sacrifices performance - particularly when small reference commands are issued. Within this paper, the above issues are addressed using generalized predictive control (GPC). A 3DOF longitudinal model for a generic hypersonic vehicle, which includes aero-elastic-propulsion interactions, is used to illustrate the ideas.