I don't think I've ever been as uncomfortable watching an episode of Star Trek as I was watching Macrocosm. The virus was disgusting, in particular the way flies flew out of the crew member's necks. I also didn't care for "action movie Janeway." It seemed like the producer's were trying too hard to copy Ripley from the Alien films with Janeway in this episode (Note: I'm not a fan of the Alien films, but I was just making an observation). Oh and, before I forget, the Tak Tak were extremely annoying. I hope Janeway blew their ship to pieces as soon as Voyager became operational again.
I did enjoy all of the scenes with the Doctor, and I thought the flashbacks to the crew being infected were interesting. And despite some of my gripes, this episode was exciting at times.