I agree that it would be more fun to design your custome and have it made by the replicator, but seeing how they have a replicator energy shortage wouldn't it be more prudent if the holosuite generated the customes for now? I do feel like the doctor should have been in custome though. His goal was to basically infiltrate the holoprogram to get Chakotay, Tuvok, and Kim back. It would have been more exciting to see him "play the role" and try to fit in while pulling off his mission!
I liked their choice of actress for Freya too. She didn't have the most exciting part, but she died well!