Ideally what I would like is a practical alien when near the cast or interacting with them, perhaps with some digital overlay for certain elements. Have a CGI-based model that literally mimics the practical alien so when the alien needs to perform a movement that a guy in a suit cannot, you have the individual in the suit begin the initial portion of the movement and then follow it through in the next frame with CGI. They should be able to do this seamlessly but you could utilize lighting/camera angle tricks to make it more believable if it looks somewhat jarring. Basically only utilizing the CGI for the portions of the movement that are literally impossible for actor to perform but you start and end the movement with the practical version.
This I would prefer to pure CGI but maybe its not realistic. I don't know much about the subject matter, just spit-balling ideas on how I would like to see it done.