Drug companies today seem to be moving away from trying to discover the next big chemical drug and moving towards biological drugs. So, for example, instead of a patient taking a pill (chemical drug) to treat a disease, the patient would be injected with antibodies (biological drug).
This shift in focus would suggest that training in drug discovery today should focus more on biological drugs and not chemical drugs, because that is where industry is headed. Of course, companies are hoping that this shift towards biological drugs will be more profitable. Whether biological drugs will be as or more successful than some of the blockbuster chemical drugs that have come out is slowly being determined.
The future of stem cell research and its applications, I think, are wide open. You would only be limited by what the laws in your country allow you to do, your imagination, and your resources.