I agree with most all your points. A lot of those elements involving would have been fine for me if they eliminated some of the mistakes in the story. I didn't find nanomachines to be that big of a deal, it's probably the laziest plot device in the series. But if the developments of the characters were great besides that, it wouldn't be that big of a deal for me. I was kind of amazed that this game mostly got a pass, compared to other big sequels this gen, that did not.
Here's a couple more that bugged me.
1) To me it seemed Raiden being a Super Ninja was silly and a response for the people that didn't like Raiden in MGS2. Maybe he was a bit whiny and not as bad ass as Snake. But, I thought he was a good fleshed out character (not everyone can be a bad ass), and this game just made him a bad character.
2) Meryl and Akiba, I mean after MGS1, who wanted meryl to marry the guy who was a one line joke of diarrhea. I understand, that Meryl didn't need a happy ending with snake. But, making many peoples favorite girl in the series marry diarrhea boy is just unsatisfying particularly with the dialogue it took to get there.
3) I felt the the game shoehorned in characters from the previous games, and essentially ruined them. in some form.
I personally gave this game a 7 or 7.5 out of 10. Which is still good, because the gamplay there is fun, and if there was a more substantial amount of gameplay I'd give it an 8.5 or 9/10. Just everything else, and length of gameplay take it down for me.
I see how people like it though. Don't get me wrong. Peacewalker was great, except that the controls were worse than all except for MGS1. Not excited for a sequal after MGS4 though in plotline.
