I personally always prefer email. It's so difficult finding times that match up to Skype especially if working 9-5. Because of that, I only skyped once with my supervisor when the dissertation planning began. This was also something that, looking back on, I regret. I think the best option would be for supervisors to enforce having skype sessions at least two or three times in the year, because it would help. Apart from that, asking the student what form of communication is best for them works well for the rest of the year.
I think really trying to set up a few skype sessions for "major" times is really important. Maybe once for proposal/ethics writing, once for recruitment and once for data analysis. I think these are the critical "times" and students really would benefit from a conversation where they can ask questions they may not realize they have.
Email can be best for quick, smaller questions that permit a quick answer.