I understand the feeling, I don't feel as comfortable speaking over the phone as I do in person. Just practice your phone technique, be sure to speak clearly and loud enough so that the interviewer will not have trouble understanding you. Look over the sample interview questions that should have been sent to you, if they do not do that then research common ones on your own, and write out an answer for as many as you can. It helps to come prepared with examples and anecdotes to be used when answering questions. My interview ended up being over the phone and it was exceptional. My interviewer and I found alot of common ground and he was extremely impressed with me. If you have not applied to the Academy, be prepared for a question about why NROTC over the NA and one about Navy vs the other branches. If you make sure your answers are well thought out then your decision will be respected instead of seen as lazy if your interviewer is an Academy grad like mine was. The same goes if the situation is reversed. Say you applied to both NROTC and NA with NA as your preference and your interviewer is an NROTC grad. Think about how you would address questions about your decision of NA over NROTC in a way that does not demean NROTC in the process.
Just be prepared, if you're prepared then you'll be confident (but not cocky) and confidence in your beliefs and in your answers creates a powerful, memorable image for the person on the other side of the phone call. I received an AFROTC scholarship so an interview over the phone is certainly not a disadvantage as long as you don't allow it to be.
Just make sure you're professional as possible; lots of employers now do interviews via phone so it apparently works in recruiting people.