As is well known in the laboratory and FDA policy communities, the FDA has generally let laboratory developed tests (LDTs) operate under "enforcement discretion." This means the FDA believes it has the legal authority to regulate LDTs (for example, through 510(k)'s and PMAs) but the FDA declines to routinely require such review - "enforcement discretion."
DTC LDTs Viewed Specially by FDA
So long as Theranos' tests are slowly working through the FDA pipelines, they are still mostly LDTs.
In a policy announcement in 2014 regarding the regulation of LDTs, the FDA explicitly stated (in footnote 4) that direct-to-consumer tests do NOT currently fall under enforcement discretion. The FDA document is here. Footnote 4 at the bottom of page 5 states that FDA won't give enforcement discretion to LDTs of the "direct to consumer" type.
If the FDA follows its own text to the word, it would potentially handle DTC Theranos tests (say, in Arizona) differently than physician ordered Theranos tests (say, in California). The ramifications of this policy footnote could roll out more broadly than just the Theranos lab, as more states pass broader DTC testing laws.
Typical 510(k)'s Are Reviewed in 90 Days
Typically, 510(k) tests, which most clinical chemistry tests are, are cleared by the FDA in 90 days once a full acceptable information submission is provided. Theranos' many tests seem to be taking much longer than 90 days, since Theranos has stated for a long time (for many quarters) it has been submitting its tests for FDA review.
FDA Can Choose to Focus on Collection Devices
There are multiple examples where FDA has focused on collection devices used for LDTs rather than other aspects of an LDT. Theranos (here) is just one more example of this FDA approach. For an October 27 WSJ article, here. For FDA documents, here and here. From these links, there seemed to be a difference between Theranos viewing the Nanotainer as a Class I device, and the FDA considering it a Class II device. From 21 CFR 862.1675, there seems to be no question that a blood specimen collection device is a Class II device (here). For example, "Device: Blood specimen collection device. Classification: Class II."
For fans of the Interstate Commerce Clause (Constitution, Article 1, Section 8), FDA has noted that the device is shipped in commerce between California, Arizona, and Pennsylvania.
23andMe: Hereditary LDT Tests Skip 510(k) Based on Posting of Adequate Public Validity Information
In announcements on October 27, 2015, the FDA has proposed that many hereditary recessive genetic tests may be offered as Class II devices but without a 510(k) review, if the laboratory publishes extensive accuracy information, clinical validity citations, and appropriate consumer education and warnings (FDA information collated here.) This is interesting in light of Theranos' decision to post more validity information in the near future (announced October 27, 2015 in the New York Times, here.)
An inventory of some public articles about Theranos is here.