Metroid vs Mega Man
Connection:
Both are purple video game psychotic killers with a personal connection to the heroes (Samus Aran and Mega Man X respectively) that worked with a law organization (Galactic Federation and Maverick Hunters respectively), even being responsible for molding the the hero's path at the beginning of their games with unwinnable boss fights
Both are based of sci-fi movie villains in the 70s (Ridley is based off the Xenomporph and Vile is based off Bubba Zanetti)
Both have worked under the main villains (Mother Brain to Ridley and Sigma to Vile) who commit their violent acts for personal fulfilment, rather than monetary gain
Both have come back form the dead multiple times, even receiving cybernetic augmentations
Both have successfully bested their rivals many times, and on at least one occasion would have killed them if not for outside intervention from an enemy turned ally (Baby Metroid and Mega Man Zero respectively)