If you really think Kim acted the same at the end as at the beginning, you're just not seeing what's there. It's easier to miss since Kim was a minor character.
So...what's there, exactly?
Being a minor character, most of the time an Ayala with a few lines of dialogue, Kim was just there. But if you bother to watch everyone on screen, admittedly hard to do with just one viewing, Kim just doesn't act the same.
The primary characteristics imputed to Kim in later seasons are a mild hypochondria and a mild resentment at not being promoted. Actually, Kim is also supposed to be both brilliant and a complete fuckup, but not in a comic Rodney McKay way. If Kim was really a main character this would have been a major problem in the show characterization.
These things are not green, wet behind the ears or naive. They are not suitable fodder for vicarious identification either, which may be why people don't see the difference. Not suitable for vicarious fantasy fulfilment at beginning=not suitable for vicarious fantasy fulfilment at end. No change, no "character development."
The moral of Nightingale was really, "the network suits are micromanaging us to death." That's the only excuse for an idiot plot, which only "works" because Janeway, Chakotay, Tuvok never even think of looking into the rescued aliens' story. This is one of the late appearances of "Borg and proud" Seven to hammer the point in.
As for Chakotay, Beltran seems not to have wanted to do much besides his player persona, which by the way he does very well. Voyager's setup and the rather discreet attitutde towards sexuality in later Treks meant there wasn't any fallback for him. Again, if you try to watch everyone on screen, when other dialogue and action is taking place, Beltran doesn't usually react if he doesn't have lines or action himself. People love to bash Wang's acting, but he usually acted like he was in the scene, even without lines or action. But then, most people talk about "wooden" performances, and to my eyes Wang wasn't that either. I almost never see criticism of Wang as hammy.