Yes, that's true, the artist's choice is thier choice, but (condensed from an earlier post I made) video games are a unique art form; they need your involvement to function, and many see the artistic integrity of video games comprimised due to design changes either during creation that differ from what the original creator originally intended/through DLC that changes the core mechanics or through the fact that video games, much like most movies and mainstream music, is made first and foremost as a product designed to get money over being an art piece. Look at Pheonix Wright for example; the original creator only wanted to make the first three games, but Capcom said no, booted him from the project and kept making it. You can see why some people don't really view it as 'proper' art in the sense of having integrity.

The 'need your involvement to function' part gives people a sense of ownership, of entitlement, due to the unique nature of video games, one that admittedly is not really fair, but is there. Most games fall into two broad categorys; you take on the role of a character, or you take on the role of yourself in a game world. The latter is why character customisation exists; a lot of people want to play representing themselves in a certain way eg. a black woman may want to be a black woman in the game because it makes her feel more comfortable. Sexuality isn't as cosmetic and obvious, and most of the time irrelevant...except when romance is a feature. In this case, being able to realise yourself in one way, but not another, can create frustration, discord - loss of immersion. For some it can remind them how simply not thought of they are - others take it to an extreme and see it as an outright sign of them not being accepted. This is why people voice thier opinions on this so strongly; because they feel they aren't being acknowledged as members of society in a game that acknowledges a large amount of it, and caters to thier particular needs (mainly through the character creation). Some people need that acknowledgement that they *are* a normal part of society, and some just want to take part in a mainstream experience without feeling like they are somehow 'different' from everyone else.

Nintendo is perfectly valid in choosing to not change thier product to reflect the wishes of some of it's players, but at the same time Nintendo - and many large games companies - make thier games with profit in mind first and foremost; even Ubisoft's Child of Light was designed to look like some pretty Indie game to capatalise off more legitimate artworks because those are selling. The artistic vision is there, but it'd be silly to pretend it legitimately outweighed the profitability aspect of the work. If that was the case, the artistic integrity of Mass Effect 3's ending would of been defended to the death of EA itself. What Nintendo's done is it's decided it costs too much to alter the game now, so in the sequal will make the nessecary allowances because it knows there's money in it. That's all; there's nothing to do with art there.
Don't be silly; NEED MOAR POKEMON AND ZELDA AND MARIO CHARACTERS YO! Wtp Magikarp and King Boo, yoooooooooooooo!