Ninjas doing missions for money, like you said - I wouldn't say I "miss" it since it basically only came up once in the series' beginning but I regret that the story didn't develop into that direction. And the whole Gato thing - I thought it would be interesting for ninja to encounter more people like him, that aren't ninja and don't even live among ninjas. In other words, I regret not seeing more of that world Naruto is set in.
Seriously, their world is, well, rural, no big factories and such, yet they have many modern things that should be factory-made. Where do they get those? How do they produce electric power? What is beyond the borders of that map of NV? I do have a headcanon about these things but it's just what I believe.
Other things I miss would be:
-the way Kishi drew hair back in Part I, it just looked more realistic, in Part II they all seem to just have spiky masses of something on their heads (often physically impossible).
-thrill from small fights with people overcoming odds when facing dangers way beyond their level. That sense of danger from mysterious enemies like Oro. Don't get me wrong, I like Part II enemies too, but with good guys that aren't helpless anymore it's not really the same. It's probably just me being a horror fan, but for me, a bunch of weak, inexperienced kids facing mortal danger (in the Forest of Death for example) is more thrilling than just strong, competent fighters opposing each other.
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Even though Naruto isn't sci-fi, there were still moments back in Part I and earlier in Part II when some new kinds of powers left me in awe. It's pretty much gone now as everything seems to be possible, even reality warping :|
Among characters I don't really miss anyone in particular, I mean I can always re-read parts if I want to see more of someone. But I still can't quite get over the death of Fu (which was like four years ago). Re-reading that part is always painful to me, the way he screams is just :NO:
_@:
