AerospacePro.com has a number of commercial flight simulation and analysis tools, most of which are in Matlab/Simulink.
Their Flight Simulation Suite is an extension (or an alternative) to the Aerospace Blockset. It includes models for aerodynamics, propulsion, mass properties, sensors and equations of motion.
They also offer an Almost Ready to Fly Simulink simulation. It's a basic model that just needs to be customized to your needs. Included in the price is a few hours of customization. Very innovative and a quick way to get your simulation flying.
They offer onsite training as well as offering free videos on various aerospace engineering topics.
The prices are very affordable.