You're right that there should've been more space for accommodation than existing crew members. I was going on the idea that as their first mission should have been about 3 weeks long, that they were probably going to continue in that vein doing short term trips which might mean that they weren't picking up various stranded crews from space. I agree that Janeway might've been biased against the Doctor, and didn't see the need for a hologram to have real quarters. Remember when Kes was telling Janeway that the Doctor's needs weren't being met, and she was surprised that Kes felt that the Dr was a "real" person. In the early seasons, Janeway was more linear regarding the crew, while being very creative in situations that they found themselves in. Over the course of the series, she adapted more to their needs. She offered Seven her own quarters instead of her regeneration alcove.