The discussion to remove ordering methods was during the sprint. 

There is a disconnect between QiiTa and QIIME, but this specific aspect was discussed toward the end of the sprint. Namely, being able to easily go from a BIOM table back to the specific sequences that are associated with a sample/observation. And, since we're going as far as making this capability available in QiiTa, we should just make it natively available in QIIME as it enables a lot of awesome analysis.

There is no intention to leave you in the dark, and was not aware that this was the case. The design goals of QiiTa from a data structure level are to represent sample metadata (stored external to BIOM), heterogenous -omics data, multiple types of observations of that data, to reasonably allow meta-analyses, and to reasonably allow questions such as "what sequences are associated with this sample/observation pair?". QiiTa additionally will comprise a web-layer and API, but those are external to this conversation as the critical component here are data structures that scale for sequences, observations and BIOM tables. As such, it really is actually important to develop the demultiplexed and observation map format along side, but AFAIK, this present structure should be sufficient. The alternative is to cram these data into specialized technologies which are tedious and possibly don't offer any real benefit (for these particular data), and limits our ability to cleanly make this type of awesome capability available to the broader QIIME community.

I agree loading a single shot is likely more efficient, but I do not think it will offer a tangible performance benefit except in niche cases, and it comes at the sacrifice of efficient random access to samples, and subsequently forces us to always load a table completely in memory if we want to do anything with the data. The existing BIOM use cases are still valid and supported -- the additional structure in the on disk organization allows for additional use cases that are not easily supported by the flat COO structure.