IMO, Khan made a great villain because although he had a sob story of his own, he didn't dwell on it. He was simply crazy from that isolation and took sheer delight in destroying as much as he could. He was bad, and he was unrepentant.
He had no Grand Plan, just took what opportunity presented to him.
'If the Apocalypse starts, beep me!' - Buffy Summers
'The sky's the limit.....' Jean-Luc Picard, 'All Good Things'
courtesy of Saquist