My wife is half Chamorro and half Japanese, so on her side of the family they generally have two questions. Is the paternal ancestor European or Chamorro, and how much European blood do they have? On top of that, a sane admixture result (how much Japanese, how much Chamorro, how much European) was desired, so that reasonable guesses could be made as to how far back the European blood was introduced.
We ran into the issue first with Ancestry DNA. They had her mostly Asian, and a hodge podge of other assignments. Dissatisfaction with the admixture results from Ancestry led us to export the data from Ancestry and put a copy of this data up on gedmatch. Testing different Admixtures with the gedmatch tools made it clear that without a reference population of Southeast Asians/Oceania, then any real attempts to separate these two was not going to work. Ancestry DNA evidently has a Polynesian reference but not really a true Austronesian reference, which really is needed for any people populated by the Austronesian expansion.
Nat Geo Genographic was pretty excellent. They have a Southeast Asia/Oceania reference population, and it has my wife with about 53% Asian, 36% Oceania, and 9% European.
Upon transferring that data to Family Tree DNA, that separation has been lost. She’s now 80+% Asian, 9% European, and 1% Native American.
So, in short:
Ancestry – probably OK if you’re Polynesian. If you’re Melanesian, Micronesian, Filipino, Vietnamese, from New Guinea, Ceylon, or Madagascar, probably not.
Net Geo Genographic – the best of the three, with a sane reference population
Family Tree DNA – in terms of admixture percentages, not worth it if you’re descended from Austronesian people.
Note: my wife, in various gedmatch tests, often turns up substantial percentages of Siberian blood. The Siberians are the population from which Native Americans came, so the 1% Native American says that there are still traces of genes found in Native American populations.