On my Air, FaceTime seems to use significantly less CPU than Skype (for video calls), so I don't have to listen to my Air's fans spin at 6000 RPMs ten minutes into a conversation.
IMO, FaceTime being pre-installed on all new MBPs (and being included with Lion) is going to make it an easier choice for a video chat with someone that's never used Skype before. (i.e. "click the FaceTime icon on your dock and enter your email address" vs "launch your web browser, go to skype.com, download and install the latest client and create a free account.")
To me, Skype and FaceTime are both good tools, each with their own pros and cons. I'm glad there's another choice.