The issue's not as clear cut as it's usually made out to be.
For one, it's only natural to have different sets of standards for men and for women. Think, for example, of a "dominant, independent and aggressive" man: push the stereotype to the extreme, and chances are you'll think of someone like John Matrix (or, for that matter, any of Schwarzenegger's roles

). But think of a dominant, independent, aggressive woman, and you'll probably come up with someone like Nikita. Same description, but very different archetypes.
Naturally, not everyone has a similar mindset. But for those who do, it's less a case of blatant misogyny than it is a case of simple character dissociation, and it's as much the result of our considerable cultural baggage than it is the result of a simple morphological assessment: women simply don't have the physical build to permanently vie for the role of the tough muscle man we've learned to idealize. And of course, from a historical standpoint, women have never really been associated with strength or aggressiveness. The opposite is also true, for the same reasons: men don't really have the same presence as women in roles that require more subtle or seductive qualities. It's not that they don't, but it's not of the same kind. Hence the common denotations of 'masculine' and 'feminine' qualities.
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Of course, you could tell me that what I've just written precisely
describes misogyny. Yet all I've established are the most common distinctions people habitually make between men and women. You could tell me, then, that this was because the general societal outlook on gender was in itself misogynistic: and to this I wouldn't really have an answer, because I really don't know whether or not it's true. But you could go even further, in fact, and tell me that it was precisely why traditional norms of 'masculinity' and 'femininity' should be replaced, since they are inaccurate and fail to convey a necessary sense of equality.
Well, in that case, let's replace them. But replace them with what? Replace them with nothing? Of course not -- you can't pretend that men and women are absolutely identical. So we have to replace them with something, in a sense, better. But how do we know that the new norms we've chosen are better? What do we base ourselves upon? Our culture? No, because we've just said that our cultural views are inaccurate. What, then? Scientific fact? But what's scientific about all this? Does science really have a criterion for what
qualities are 'feminine' or 'masculine'? No, it doesn't. So, in essence, we have nothing to base ourselves upon. Strip away our cultural baggage, detach us from our age-old interactions with women, and we really haven't got any idea of what we're doing. We're just throwing shots in the dark.
So, you see, this is when the line finally blurs. When we stop making the difference between gender
equality, and gender
identity. Between innocent differentiation and harmful discrimination. Confuse the two, and you've gone past the point of no return.
I've gone far, far off topic here, but it's only to prove a very important point:
misogyny is an incredibly relative term. I'm not saying that misogyny doesn't exist: it absolutely does, and it is something that must be fought against. But there's just a point beyond which the word barely means anything anymore. You could call any man-woman distinction a case of misogyny: you could keep arguing for and against it, but you'd still have an entirely meaningless discussion in the end.
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Time to actually answer the question

.
Are all Japanese developers just misogynistic pics? No -- at least, not all of them. But I think you expected that, so I'll give an example.
Metroid: Other M was caught in a whole string of more or less accurate accusations of misogyny, but I don't think that was what made the plot seem so lackluster. After all, Other M was made by the same man who had created Samus in the first place. Instead, I think it was simply the result of a failed attempt to give some added depth to Samus's character; in the end, though, her poorly-managed characterization just came off as unnecessary, and the game's relatively convoluted plot only made this worse. The game tried to humanize her by giving her a sense of vulnerability, but the latter aspect was overblown at the expense of the former.
The 3rd Birthday? I can't really speak about the plot, since it's not exactly very conventional. But I can tell you that the clothing damage that was implemented makes this a very Japanese game, and not in a very good way. I can promise you that clothes don't actually get damaged like that.
And yes, pretty much everything related to clothing damage, breast physics, panty shots, and overall fanservice could go down as misogynistic. But remember that the devs aren't the only perpetrators here: they're only including what their general fanbase would enjoy. Food for thought.