Robot DNA: Introduced in the late X series, we are shown that X, Zero, even simple mechaniloids have DNA. Therefore it seems a safe bet that classic series robots also have something resembling "DNA" programs in them. In the ZX series, humans and reploids have machine bodies and lifespans, and we are told the differences between the two species are negligible in an everyday sense. They seem fully able to have families together as well, and both humans and reploids are capable of being transformed into cyber elves. It is plausible then for the sake of inter-breeding that some manner of human DNA and reploid DNA conversion has been developed, and that machine-body organs have been developed for the purposes of sex and childbirth. In the Legends series, carbons which are extremely human-like beings far descended from reploids are shown to respond to sex both recreationally and reproductively and give birth in the standard human way. In Rockman Xover, all timelines and alternate dimensions of Mega Man literally cross over in a dimensional bubble nexus known as the X-Over world (cross-over world), where any character can meet any other character and all the technology across the distant universes can be shared and are integrated.

In summation: No matter what Mega Man character you are into, future technology canonically exists in the cross-over world that would allow you to have sex and make babies with it. (You're welcome.)