Thinking about it a little more, I think that crosses were largely phased out, or at least pushed to the background, of the show because the cross as we know it is inherently religious. It's pretty much the quintessential symbol of faith and religion.
Buffy and Angel have always steered clear of religion in their episodes and seasons (which I'm thankful for, big time). The Master had some pretty strong religious undertones to him but beyond that, they didn't mix with religion much at all, if ever. Crosses don't really mesh with that direction.