that 90% of all evil world/galaxy/universe domination plans involve destroying all other life in the world/galaxy/universe? That has got to be one of, if not THE WORST plan ever. I mean, what's the point of taking over and killing everyone if after it, it's just gonna be you and your army? Doesn't that just make things boring? What's the point of being in charge if there's no one to rule over? The things that keep me up at night...
Yeah... That does seem boring. :/ Or maybe they like the loneliness and solitude and don't give a care. Or they want a bigger solitude to live in than what they have now. The screams and the sobbing and the boo hooing might get tiresome after a while
Wipe out the opposing force and all future opposing forces and take all the glorious loot. It's really a resource game. It's like the way they killed the Native American's for gold and farmland and expansionism and all that stuff. It's really the most logical plan short of mixing the species/races together to form a larger empire.
Most of it is to make the Big Bad/Villain a Complete Monster so then the Hero seems more Heroic when Good triumphs over Evil in the end. If the Villain of your story is a genocidal madman, well, it's hard to like a person like that that has crossed such a glaring Moral Event Horizon as killing off entire races. Also, like Jiku said, it's to remove competition and to make examples of. 'I wiped this race of people out of existence, I can do the same to yours if you don't know your place!' The less opposition you have the more likely you are to succeed in your goals.
I can't stand villain plots like this because it comes off as being a villain for the sake of being a villain, with no real motivation. In the end it's just a poorly written character.
But all the glorious loot. Don't you want mad loot? Have you never farmed items on the lives of low level enemy npc's? Same concept except actual populations never respawn.
They also could start a new world where he just impregnates all the honeys and gets the population going again.
Then you run the risk of one of the said offspring rising against you. Also running the risk of one of the Mothers rising against you. Or, worst case, all the Mothers rising against you.