First, Scouts may see this as potential a way to get badges without having to do all the work. Second, undesirable individuals may seek to use this as a method to make contact with Scouts. Oversight by the Scoutmaster and a thorough review of the counselor's abilities and intent are excellent ways to prevent the above two problems from occurring. Also, the Scout should be told that if he and his counselor do decide to meet, the Scoutmaster should be told before the meeting is scheduled to take place. Long distance counseling is potentially an excellent boon to Scouting.
Many merit badges are hard to earn due to a lack of qualified counselors for that subject.
Railroading merit badge, for instance, would require a counselor with experience with model trains. Even though you may not be able to find an adult locally who would be able to help out, it might be possible to get someone with the National Model Railroad Association to help. I don't know how they would feel about working one on one with a Scout but promoting model railroading is what they're all about. Finally, not all subjects are appropriate for long distance counseling. Merit badges with a lot of physical requirements, such as Swimming or Sports, may not be good candidates for long distance counseling.