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How do you make it not feel like a "shock factor" gimmick?

It is a bigger problem than sex.

I don't even care about any of the cardboard cut-out characters in the vast majority of games I've played, and I'd care even less about any "sex" these characters may have than I would about seeing two mannequins portrayed as humping in a shop window. I certainly don't want to have to sit through it and pretend to care.

There are a lot of emotional basics that need to be covered before you can meaningfully include sex and not be seen as including it as a "shock" or "gimmick".

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There are a lot of emotional basics that need to be covered before you can meaningfully include sex and not be seen as including it as a "shock" or "gimmick".

When I was playing DA: Origins, the relationship I had with the Bard had a pretty cliche process, but the actual romance scene was remarkably well done. It felt conclusive and "earned". There was no way it could be shocking or a gimmick, because such a scene was heavily foreshadowed.

The key word here is "foreshadow". Make it clear that the characters have a thing going on, and maybe even include a warning for players that they may soon see some bouncy-bouncy, and they may want to... *sigh*... skip the scene.

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There are a lot of emotional basics that need to be covered

I would say compatibility is a big one, and is not really an emotional "basic". Back to DA, Morgan was tough to get along with because she was kind of a bitch. Since the characters were so well developed, I had to "change myself" to go further with her.

If you have the player change their standards for the sake of a fictional character, you've got something seriously immersive. In that case, sex becomes pretty forgivable from a common standpoint, I would imagine.

it's a sad fact that sex cannot be portrayed in games the same way they would be in film.

take the game 'Quantum of solace'. the movie has a clear sex scene which is perfectly accepted. However, if the game featured the exact same sex scene it would almost seem awkward.

I believe it is because sex IS featured to much in film that it is just acceptable, in some on-screen relationships even neccesary, to have a sex scene.
Whereas in games, it stands out because it's not a common accurance.

Based on this, I feel there are two ways that sex scenes can be handled well in games. At least before it feels less of a big deal.

The first is what god of war 3 did where they went all out and really MADE it a big deal. It understood that it could be jarring so they made it deliberatley quite in-your-face. This works because it feels like it would have felt exactly the same, be it in film or game.

The second is to only hint at the characters in question having sex. Show them waking up in the same bed together, this way, there is no awkward sex scene, but the idea and the character progression is still there.