I've been in the closet about this but I think now, I should come out with it.
I'm a puzzleshipping fan. Yes, I think Yami (Pharaoh, Atem, whatever names he goes by) and Yugi would (should be and are) an amazing couple.
I feel that people in a relationship, and if it works out, it's not about sexual stimulation or how great the sex is, it's about the two being complementing and making each other feel whole.
Yami, or Pharaoh Atem (as we learned his name, and he did too in season 5) he is the darkness to Yugi's light, the seme, as some people might put it. He is the spirit of a king of Egypt, which makes his protective nature ancient and also part of his nature. He will (which has been proven many times) will do anything for Yugi, even went as far as to protect the young ones mind. Yami has even agreed that Yugi calls all the shots, he won't make a decision without talking it over with Yugi first, and a promise he made to Yugi, giving the relationship neutral ground.
Yugi, a high school student and the chosen one to the millennium puzzle, which to me means the pharaoh, and fate, chose these two to be together. He's the light to Yami's Darkness which is why these two complement each other perfectly. Yugi, as most would put it, is the uke, but control over Yugi's body is shared, not fought over. Like the other dark spirits of the show (Yami Bakura, Yami Marik) power and control is shared, such as it would be in a healthy relationship.
The loses, however, seemed to be proven much greater. Yugi sacrificed his soul to the Seal of the Orachalcos to spare Yami even if he went against his advice, something Yami told him not to do. When Yugi was taken from the Pharaoh, he fell into a state of depression and angry. Even taking the frustration and anger out on Weevil, the duel is well over and Yami had one, but he just keeps attacking the kid over and over again. Yami even visits the valley of lost souls to talk to Yugi and Yugi plans the whole duel to rid the darkness in Yami's Heart, something that only someone who loves someone else in return would be able to conjure up. Even during the Ceremony duel, Yugi hesitated to make the final call and win the duel, not wanting to lose the Pharaoh to the afterlife. He does make the final blow and falls to his knees sobbing. These events showed just how close of a connection both males have,
Yami and Yugi, have gained much from both parties as well as lost. Yugi learned to have confidence and to stand his ground, while Yami learned the power of friendship and to suffer wins, you need to suffer loses. Winning isn't always important.