I know that if it hadn't been cancelled, he wouldn't have killed Wes, as he wanted to do more stuff with Wes and Illyria in the next season. But it's Joss, so he'd probably feel he needed to kill SOMEONE off without a really good reason to make it all dramatic and stuff. That's just what he does.
I not really sure but I think the whole Illyia storyline was supposed to be Joss's attempt at the Dark Phionex storyline. Something he tried with Willow but seemed to be getting right here