The evidence of desertion is strong, leading many to question the long delay in the investigation. The impression has been that the Administration did not want to address the growing criticism of Taliban leaders with terrorist ties for a deserter. There has also been an allegation that lives were possible lost in missions that included searches for Bergdahl.
I have previously said that the Administration clearly violated federal law in this swap. The fact that Bergdahl is now viewed as a deserter is likely to rekindle the controversy, particularly over the allegation of possible lost lives in searches for Bergdahl.
For a discussion of possible defenses, see this earlier posting.
Normally, the fact that he suffered through five years of captivity with vicious terrorists would militate in favor of a lighter sentence. Article 85 makes desertion a crime that is punishable with up to five years. Article 99 (misbehavior) includes a maximum of confinement for life. That would give the defense a great incentive for a plea but the prosecutors may be sensitive to the prior allegations that the Administration has been delaying the case to avoid an embarrassing prosecution.