This was my favourite Escape Pod episode in a long time. It was nice to have a fun story, especially after having just listened to "Mantis Wives" yesterday.
As has been mentioned, and maybe this is due to Alisdair's accent, this made me think of both Hitchhiker's Guide and Red Dwarf.
Dylan is the Arthur Dent: the everyman: completely out of his depth, but doing his best to roll with the circumstances anyway. He's not particularly good at anything, but he is at least one of the least screwed up people around. I think a lot of people can relate to that, and I think it is what makes characters like Arthur Dent or Richard Mayhew stay with me long after I have finished their stories. I think Dylan may stay with me for awhile too.
Captain felt to me like a combination of Holly and Xaphod Beeblebrox. He is clearly competent to run the ship, hence its continued existence, but comes across as a bit of a fool all the same, and you can never quite be sure if he is being genuinely foolish or merely playing at it for Dylan's benefit.
One thing that occured to me while listening, is a possible attempt at a solution to the mental instability of the would-be colonists. Were I Captain, I would start shrinking all of the individual instances together to force the personalities to interact. In time I am sure many of them would be able to re-adapt to being around other people, and the ones who could not would simply be re-isolated.
Plenty of people have antisocial tendencies, I know I certainly do, but for most of us it is simply impossible to adopt a hikikomori lifestyle. The desire to have food and shelter overrules our desire to not have to interact with other people; we force ourselves to do things we do not find pleasant or attractive to avoid things that we find even less pleasant. I suspect that, if forced, the colonists could be re-trained to do the same thing.
The solution employed in the story is not a bad one though, and it is almost certainly what I would try if my first idea failed.
The only other thing I would do different is offer Dylan the chance to be decanted for good instead of just being copied like he had been before. I'm not sure what the difference would actually be since the POV Dylan is really just a copy of the original flesh and blood Dylan anyway, and destroying his file(s) would be the same as what is eventually going to happen to him anyway, but it seems more humane to me to at least give him the illusion of a choice.