My wife and I serve independent of a formal mission agency. We have generally found this good… but not all of the time. There are down-sides as well. I feel this link below does a fantastic job of looking at the pros and cons of this. The primary writer is an independent missionary, so it is more “pro” than “con” but still seems fair.
(Of course, sometimes the wrong people go into the wrong missions for the wrong reason. Independence is their way to circumvent a beneficial selection process. The advice to join with an “open” agency that takes seriously training seems like a good idea— although I have seen things that make me doubt the efficacy of YWAM’s training.)
Collection of answers from experienced missionaries to the question: Why do some missionaries serve independent from an agency?.