that is my feeling too. princess masako has accompanied prince naruhito for official engagements in japan already (and that trip to The Netherlands). if looks can be gauged, she looked well. i think the IHA is prohibiting her from too much official engagements for fear that she might be too popular to the japanese people and will have the Diana effect.
if her stress disorder is not genetic, three years is awfully long to be sick with it and not recover. adjusting to protocols must be hard, but she chose to stay in that life and intelligent enough to figure things out, that can't be the case. there is already an heir, what else is left for her to be stressed about?
if i have to do a conspiracy theory, the IHA is trying to get rid of princess masako, but can't because prince naruhito is the crown prince, so now, they're trying to break her spirit and designate her to stay in the shadows.