I've done this twice now (they don't do onsite, probably because of location) and I was really happy I had to the opportunity to do this. It was a really great way to see if I hit it off with the PI's. You can only gauge so much from email exchanges and their research about their personality. I think it's a good way to see if you guys are on the same page research and personality wise. I've had several friends do formal interviews via skype instead of onsite because of location and they both got into their top schools. From what I gather, schools take these skype interviews as serious as onsite ones. So I wouldn't worry about it not being equivalent to being there in person!