Some sort of conclusion fallacy or just a non-sequitur

No fallacy that I can see. In fact, it is a strong argument but ONLY IF one is providing reasons that alternative medicine is effective is because traditional medicine is problematic.

It looks like a group of statements, proclamations, without any reasoning from one to another and none intended. You could add the sky is blue today, and any other statement. It is still meaningless.

The guy is merely pointing out that due to current issues seen within the healthcare system does not mean that altertantive medicine is any more effective. 

“Problems in medicine do not mean that homeopathic sugar pills work; just because there are problems with aircraft design, that doesn't mean that magic carpets really fly.”

― Ben Goldacre, Bad Pharma: How Drug Companies Mislead Doctors and Harm Patients

The question seems to imply that a "conclusion fallacy" (formal fallacy) is somehow totally different than a "non-sequitur."

The terms "non-sequitur" and “formal fallacy” are sometimes used interchangeably because many people consider all formal fallacies to be non-sequitur. This brings up the issue of what the official authority is for defining fallacies. What organization enforces compliance with the definitions of logical fallacies? Stating that many people consider all formal fallacies to be non-sequitur fallacies doesn't make it true, that would be the Ad populum fallacy which claims that something is true simply because a large number of people believe it.

A non-sequitur fails (fallacy) to establish a logical connection between the premise and the conclusion. If it fails, then it's a fallacy.

People often use the word "logic" to describe an attempt at logic, and most attempts at logic completely fail. Random and meaningless statements that have no causal relationship might be incorrectly referred to as "logic" when they're actually an illogical communication. An attempt at logic is not necessarily logic. The original post is a communication . It's not even an explanation , because the word explanation implies valid logic.

A fallacy is a failure. I ask the question, "Is there a failure in the communication?" If there is a failure, then there is a fallacy. And if there is a fallacy, then call it a fallacy. The conclusion in the post is not a consequence of the previous statements. The conclusion fails to follow logically from the premises. (Non-Sequitur) If there is a failure, then there is a fallacy.

The reason why some people might think that there is no fallacy is because the premises don't disprove the conclusion. But don't confuse a failure to disprove the conclusion with a valid conclusion. It's not the same thing.

This isn't a fallacious statement. The person is stating that the administrative issues with the healthcare system have no effect on the effectiveness of alternative medicine. A less politically charged equivalent would be something like "I can't find a good mechanic to work on my Audi, but that doesn't make your Volkswagen go any faster."

If someone was to make the opposite claim, though, that using issues with the healthcare system rather than experimental data to prove the effectiveness of alternative medicine, that would be a nonsequitor.