Hi @colinbrislawn and @charlottejk,
I hope it's okay if I 
-in? My group did an scoping review related to this issue:
You may find Table 1 the most useful; it breaks down four techniques (closed ref OTUs, de novo/open ref OTUs, ASVs, and a technqiue called MimpLiPi) and the implications for analysis when combining regions. I'll note hte last is pretty new and I dont know that it's been independently benchmarked like other technqiues.
Our paper didn't evaluate "best" just explored what was avaliable. Based on the review, the options I think are best to consider would either closed reference OTU clustering or ASVs and then collapse to a common taxonomic level. There are advantages and disadvantages to both of these approaches, depending on what you want and need from your data.
Best,
Justine