First of all YGO is a SHOUNEN, got it? Not a SHOUNEN-AI!!! I can prove it using the Shounen Jump chapter when Jou(Joey) got a questionable tape. In the chapter, Yug and Jou were making remarks about how hey can see through the pixelations.
Secondly, Yaoi fan fics pairing for YGO is usually Seto/Jou, Yami/Hikari, Honda/Otogi. Basically yaoi fans love the pairngs of all the Yami with their light counter part. This is only fan's work, again this is a shounen, not a shounen-ai.
Thirdly, you are entitle to your opinion on this issue. The series is up to your interpretation and so is the pairing of the char. so go wild with it if you want to
Some people are big shot, some people are little shot, some people needs to be SHOT.