Something is horribly wrong with these two pairings:
Can you guess why?
Allow me to be creepy:
This explanation is under the assumption that Mega Man and Mega Man X are the same person. That being said, I don't necessary agree with that theory, but for the sake of this argument, let's pretend that they are the same. Mega Man and Mega Man X were both built by the same person, Dr. Light. Bass and Zero were also built by the same person, Dr. Wily.
Let's explore the Mega Man/Bass pairing. I just don't understand this pairing. They're enemies not lovers. How those two became popular in the Mega Man yaoi universe is beyond me, but some people find that pairing attractive. Okay, then. I'll try to reserve my judgment.
On the other hand, the Zero/X pairing makes WAY more sense. I guess I'm biased because its my favorite one and the only yaoi pairing I accept. Even in the games, there is a sense of them being "more than just friends". The games don't out right say, but there is a feeling that they love each other and would die for each other. Because of the closeness of their relationship, people question their sexuality. Even people who play the games infrequently say that there is a yaoiness to the series.
Now that I've given background, its Mega Man gay story time:
Imagine Mega Man and Bass getting together doing whatever robots do to explore themselves. Realize, if we are keeping with the "same person" theory, that Mega Man is "younger" than X and by that I mean he looks younger, he looks like a kid. As time passes, Mega Man is updated as X and Bass is nowhere to be seen, replaced by Zero as the robot to counteract X. In later years, X meets up with Zero. They both become friends. Due to Zero geting out of commission often, X starts to develop feelings for Zero. Zero has the same opinion, and they become lovers.
The fact that Bass and Zero are both "related" in creator, and Mega Man and X are the same person makes for one interesting storyline.