I don't think what you're looking for exists. I think the more yuri/yaoi an anime gets, the less the story quality is relied on, and the more fanboy/girl pleasing comes in. Not that I can say this with complete confidence, as I've never seen a yaoi/shounen-ai anime... but from what I have heard I don't think there is much difference on that side of things.
You might have better luck if you moderate your search to a good shoujo-ai/shounen-ai anime. In that instance I would probably recommend
Maria-sama ga Miteru, or for a more action oriented anime,
Kurau Phantom Memory.