I think the UI is cleaner and more Mac-like; Pixelmator felt a little too comfortable throwing consistency and OS X UI standards out the window. It's been a while since I tried Pixelmator, though, so maybe this comparison is no longer fair.

Also, though it probably won't matter for most people, Acorn's file format is pretty ingenious: http://shapeof.com/archives/2013/4/we_need_a_standard_layere...