Okay, we're dealing primarily here with the Doctor while everyone else just acts like themselves. Talking about the Doctor's character development is a bit tricky. He is a program, and therefore not someone who is supposed to develop as much as adapt. With Kes' help, of course, this adaptation has been running amok lately, and he's become almost human. This means that any difficulty in his programming should result in massive change.
Computers are only as smart as their stupidest command code.
As a doctor, the Doctor is driven to fix things, and thus seeks self-improvement, but as a hologram, there are many things his warranty just won't cover. And this is as good a time as any to mention a theory I've been working on. The Doctor comes out of Voyager's computer, and we know that this computer is made, in many places, of bio-neural packs. Such dreams can lead to destruction, as they do in La Boheme . Since we're not going to lose the Doctor, this danger gets averted by the end, but the warning remains.