Why does Imperius hate the Nephalem?

I presumed it was simply because he voted on the "destroy humanity" side of the original debate. I'd also guess that this was at least partly because the nephalem have the potential to be "greater than both" the angels and demons, threatening his power.

I don't have anything to back this up, though - just my own take on the situation.

As Raven Dreamer points out, there's also the immediate fact that he blames you for Diablo's resurrecterific rampage through the High Heavens, which is probably plenty to annoy him on its own.

Another factor of Imperius's hate is that he believes in the order of things. There has not been a change for a long time, so he is very indifferent towards everything unusual. As Melini said, he is disgusted by Inarius and Lilith's love and is restless because Malthael, in his advisory role, is unable to predict the future of the Nephalem.

Imperius believes that the Nephalem are a sacrilege in themselves which is why he is not so happy about us, the player, walking into the gates of heaven, right after his failure in the final battle against Diablo.

If anything, we can be sure he will be hating us more in the possible future expansions.