The biggest problem (for me) is that every alternative medicine I've ever had the displeasure to be exposed to hasn't just been "alternative", which I'm actually fine with, but downright fraudulent. There is no regulation of truth or veracity in claims, no standards, no way to tell who to trust. The "medicines" that succeed are the ones that can best extract money from their "patients" with the least possible cost: thus, the prevalence of homeopathy.
Throw the 90% of alternative "doctors" (that are really just new agey con men) in prison, and the alternative medicine that remains might actually be worth a damn, but my experience with the field (coming from New Hampshire, where homeopaths seem to outnumber regular doctors) is that they are, at best, grossly negligent, and are more commonly outright malicious for person gain. But they lie, constantly. About pretty much everything. Regular doctors don't have much of a reputation for honesty, but they are leagues and bounds beyond your standard homeopath or naturopath. Probably because of all that legal stuff that requires them to make certain disclosures and label in certain ways and answer certain questions, regulations the alt.med. fraudsters do not need to operate under.
I know there are many effective natural medicines - it would be nice if those were offered, but they don't make money. And with the industry in the state it's in, supporting it is either stupidity or conspiracy.