most of these points are based on the misinterpretation of the manga.
For example, "10 minutes of good made up for a lifetime of bad". No where was this stated or implied. None of obito's 'feats of good' are being used to counterbalance his 'feats of evil', the reason NAruto shows Obito respect is for the person he has become after being TnJ by Naruto. And that person is one who would willingly do all those feats of good we saw in the last 10 minutes or so. So Naruto is absolutely not saying that what Obito did made up for all the bad, he just respects the person that Obito died as and can appreciate his change from the one who did do all those evil things and tried to initiate infinite tsukuyomi. So unless you can't see that the Obito who died is a different person than the one who did all those killings, it shouldn't be difficult to see how naruto can have respect for the current Obito.
Second, Naruto forgiving Obito doesn't mean he disrespects Neji. If you read the manga, you'd know that this whole idea of holding on to hatred just results in an endless cycle of hatred which screws over everyone including the people neji cares about. Naruto obviously cares a lot about Neji which is why he was hit so hard that he almost turned to the dark side when Neji died. Neji died for Naruto and the shinobi alliance, holding a grudge against Obito won't do anything to bring neji back, it will only get in the way of their victory, and if they lose here, neji's death would be for nothing. So rather than indulge himself in petty revenge that will render naruto a hypocrite and just another avatar for the cycle of hatred to flourish, naruto is not going to hold onto useless feelings like that.
Third, Naruto is a very realistic character. A realistic character isn't a character who merely is like you or me, or a person who exists in reality a realistic character is one who would act this way had he actually gone through the things he's gone through and holds the same ideals as he does in the manga. Normal people haven't been brought up in an environment where they were completely alone and hated throughout their childhood, nor do they have it as their lifelong goal to stop the cycle of hatred and find true peace without eliminating the value of humanity in the process. However, if a human in reality did go through something like what naruto did and possessed the same goals as him, then I find it very likely that they would be quick to forgive and treat another with respect, especially when they saw what led that person to fall into darkness.
Then there's stuff like the Child of Prophecy thing having nothing to do with falsifying themes of part 1 since Neji's theme was not about defying 'destiny' it was one's ability to change their own destiny if they wanted to. Naruto doesn't have any reason to change his destiny as his destiny is the savior of the world, so those two themes don't conflict. Hard work = strength wasn't really a theme in the manga, it was always fighting for someone else or 'protecting others' that was the the theme and motivation for working hard.
The other stuff like Naruto's powers being easily obtained, or him being a puppet aren't true either. Powers such as bijuu mode and Kyuubi chakra mode did require work on Naruto's part, it's just not the normal training that people go through in order to gain powers. In order for Naruto to gain KCM, he had to eliminate all the trace amounts of hatred he had for the people who've wronged him in the past. As we've seen from the OP's comments about Naruto's morality, doing something like that can be extremely difficult to do, or even impossible for some. Same thing with using bijuu mode, Naruto had to befriend Kurama, which could only happen by Kurama witnessing Naruto's high ideals. Hagoromo's powerup might be the closest thing to a freebie, however Naruto could still only use it after convincing the other 8 bijuu to help him and after giving Hagoromo and acceptable answer.
The rest of the stuff is pretty much just personal taste.
