What can I expect from a Skype interview for PhD admissions?
This doesn't sound like an overly formal process as you're already known to the interviewer. However, in my institution at least, the process is becoming much more formal (person specifications, training for interviewers, etc.) and so there are definite areas that the interviewer will be trying to explore:


Do your skills match up with what you claim on your application? Expect specific questions on your application, particularly on relevant projects, or reports, or dissertations.
Can you communicate? Particularly, why do you want to do a PhD, why in this area, with this person, etc. This also covers language skills, if you're not a native speaker. Expect more general questions probing your motivation.
Can you link together different areas of knowledge? Show that your earlier studies have gone in and you can see where they're relevant to the PhD topic. Expect detailed questions on key techniques for this project, maybe linking back to courses you've taken (if they don't make the link, it's a strength when you explicitly do).
Do you know what you don't know? There's a lot to learn in a PhD and the best candidates will (a) know that, and (b) want to fix that themselves. Communicating what areas you need to improve, and how you want the supervisor to help you improve, can be a strength (provided it isn't key background for the PhD!). This is where you should show you've read the research proposal, and also the papers referred to in it: you don't need a detailed understanding of it all, but you should clearly show what you've understood, and how you'd go about learning what you haven't.
Evidence of problem-solving skills. Talking about projects, reports written, group work done. Show that you understood what you did (even if strongly directed), that you can communicate it clearly, and how you generated ideas.
Can you connect with the potential supervisor? This can be purely personal, and is the hardest thing to do in a Skype call. If possible, try and make it a conversation instead of a question and answer session. Also, try and prepare some questions to ask them, particularly around the research proposal.


As I noted at the top, if you're already known to the interviewer, and if there's no formal university process mandated by central administration, this could well be an informal chat. Even then, I'd make sure you've read the research proposal, and researched its background, so that you can genuinely talk, and not get a huge information dump.