you are just assuming Vergil is one-dimensional character, he has no personality except NEED MORE POWER, sure it is a priority, or THE priority of his life, but that doesn't make him a low-life "I NEED MORE POWER" broken record kind of guy. we know absolutely NOTHING about his personal habits & traits, nothing would be out of character if we know nothing about his life except his thirst for power.
he could have had a one-night-stand, he could have fell in love with someone, HE IS CAPABLE of love, love isn't something you can control anyway, or hell it could be Nelo Angelo & another she-demon. though its highly unlikely that he fell in love, I wouldn't say its out of character if the story demanded it, yamato might've been broken because Vergil was trying to protect his family like someone earlier have said.
there are other things that imply that Nero wasn't cloned, one thing is, Sanctus didn't know that Nero possessed demonic power, but he called for him as soon as he heard, maybe he knew a few things, but not enough to make him know everything about Nero, he would have used Nero a lot earlier.
Nero possessing only Vergil's arm is a working theory, its only problem is that the writers have been hiding his "origin", its a build up for something more, but it could be just a diversion, fool us into thinking the other way around.
the plot holes in those theories can be easily fixed, if there are any.
there are other things that imply that Nero wasn't cloned, one thing is, Sanctus didn't know that Nero possessed demonic power, but he called for him as soon as he heard, maybe he knew a few things, but not enough to make him know everything about Nero, he would have used Nero a lot earlier.