There's absolutely nothing wrong with having your child see a resident (I know; I work in a resident-based pediatric clinic). The only disadvantage (other than if you don't get a good doc) is that they leave after 3 years, and you end up getting a new doc. However, the advantage of that is that you're getting someone who has never seen your child, and may pick up on something the other may have missed.
We just had our last visit (normal checkup) with our son's doctor. She advised us to pick another doctor who is early in their residency. We have to choose male or female.