Most issues with hormones is that they do all sort of stuff on yourbody. not only one controlled thing
Side effects of Oestrogen-containing contraceptives that don't seem to be caused by Progestin-only contraceptives include:
Increased risk of cancer
Increased risk of heart disease
Bone density reduction
Blood clots / Stroke
Increased sensitivity to UV (and associated skin cancers)
Reduced breast-milk production. This isn't very detrimental to one's own health, but does effect the health of the child.
The only down-side of Progestin-only pills versus Oestrogen-containing pills is that it is extra important that it be taken at the same time every day for full efficacy. Obviously the implant doesn't suffer from this drawback.
also, i have a paranoia that no hormone/protein/enzyme does less then a few things in your body. if they list only one or two effects, it's because they have no clue what else they do.
prolactin was believed to only affect the milk production in mamals for a long time (and water-salt control in fishes). now there's some other dozen effects on the body including neuron fiber formation.