It's easy for most people to find something wrong with what they're not familiar with or don't understand. It makes sense that so many westerners don't 'get it' since none of them have probably ever lived in any part of east asia. Statements like I'm seeing on this page remind me that more people need to get out and see the world.

There's nothing wrong with any number feminine male characters/people. Learn to deal with it, folks, it's the way the world is.

It all comes down to cultural differences, really.
People who are not into the japanese culture, never been in japan or are die hard navy/military fans cannot understand this and hate on every character that have medium/long hair, no beard and no rough lineament.

I lived in japan, I'm what you call a "feminine" guy (what I mean is long hair and pretty face but I'm the first to say that a man have to act mainly)... but the reality is that there this compare to "handsome" and you are more likely to get tons of girls. (it works here in italy too. Many people can think "eww man, he looks so gay" but there were a lot of girls after me when I was not in a relationship)

That said, I hate the characters that are VERY feminine in videogame, the ones that have extremely feminine apparences, acts like a pussy and are 100% annoying... but they are very few. (people like Zhang He in Dynasty Warriors)

Japanese games never try to conform to the norms of political correctness. If you see a "girly" character in a Japanese game, it's because that's the art direction the developers wanted to take, and nothing else. I really respect that.
In contrast, certain big publishers, namely EA & Ubisoft, are notorious for ruining their games trying extra hard to conform with political correctness. Churches without symbols in Assassin's Creed 3 so that nobody gets "offended", gay characters that feel forced in Dragon Age 2, the list goes on.
If there is one reason that Japan is cool, it's because all Japanese people shit on political correctness. Hurray.

Yes because Japanese publishers never force their devs to do anything based on market trends or political correctness.

Just like Vaan and Penelo were featured in Final Fantasy XII for their artistic merit and not thrown in to conform to Japanese teen stereotypes...

Well yes I do see them as physically weaker because most of them are. I walk them home because a girl walking at night alone is more likely a target of an assult than a muscular man. We might have a different definition of sexist here, in my perspective women in general are physically weaker than man, more vulnerable but a man and women can be equally intelligent. That's how we are built, testosterone stimulate muscle growth more than estrogen does. 

Anyone asking for a complete gender dissolution is just fooling themselves, there are several differences between the genders, otherwise the concept of gender wouldn't exsit at all. There's nothing wrong with gender awareness, it all comes down to whether you discriminate somebody based on it. 

That's not the case at all. Quite the opposite.

Women are more liekly to be the victim of a sexual assault (although the difference is much smaller than most people think), but a man is far more likely to be assaulted in general. Even criminals have a sense of chivalry, apparently. And size means nothing when weapons are involved or when it's several men fighting against one.

And there we go.  Good post that answered the root of the question.  Many of the other responses so far seem to be following the "my personal preference are the only RIGHT way" path, which is tiresome.

JRPGs simply leaned too heavily on Japanese trends at the time for them to connect with western audiences.  Not just with "pretty" male characters, either, but also with all the Visual Kei inspired costumes and aesthetics.  Western fantasy, for the most part, is much more traditional.  There is nothing wrong with any of it.  It just has to do with what people expect, what they prefer, and what they can associate with.  Cultural differences aren't about right or wrong.

However, if someone is arguing that they are too "manly" to play an androdynous character, then I would suggest instead that they have a lot of growing to do as a person before they can get over those kinds of minor and meaningless insecurities.

Is that so? Maybe in some cases, but not in all.

Consider that a lot of people want to be able to relate to the main character, and even project themselves onto them. They want a main character who they can imagine themselves as. An MC who's an idealised version of themselves. It's aspirational.

Someone with a traditional "manly man" look and personality is obviously going to have more trouble relating to a very effeminate male lead. It doesn't have to be anything to do with insecurity or hating the MC; they just can't see anything of themselves or anything they aspire to in a character like that. For someone with more traditional values, a he-man MC is easier to relate to.

Honestly, it kind of annoys me that you clipped out the part where I said, "it just has to do with what people expect, what they prefer, and what they can associate with. Cultural differences aren't about right or wrong," and only included the paragraph where I'm talking about something different than simple preferences.

Also, most of the characters we're talking about aren't effeminate, they're simply closer to being beautiful than handsome.  Most of them kick ass.  If someone is so hung up on the looks of the character that they can't play a game, then yeah, that puzzles the hell out of me.

Of course, I admit that I have a real problem playing dumb characters, but that's because I experience a disconnect and loss of immersion when it comes to their decisions.

I responded only to the part that I had an issue with. And even when taken in context, I still think it's an over-generalised statement.

Looks rarely come on their own tho. In fictional works, they tend to come with certain personality traits and values. Hell, a character's looks are often used as a way of definining their personality and values: you can immediately tell what a character is going to act like just by looking at them. In theory, an effeminate/"beautiful"/whatever male might have a very traditional masculine personality, but in practice, they rarely do. You can blame that on lazy character designers.

This will severely limit the number of games you can enjoy.