So the get.sharedseqs(unique=) command works exactly as advertised… 
just not the way I’d like 
Consider a timecourse example. I have two samples (A and B) I am tracking across 3 time points (1 2 3). I can make nice venn diagrams comparing OTUs at each timepoint. Now I want to know what OTUs are in A1 but NOT B1 and vice versa. If I type get.sharedseqs(unique=A1) mothur will dutifully pull out OTUs that are unique to A1… as compared to A2, A3, B1, B2, and B3. I would like to be able to type something like get.sharedseqs(unique=A1,vs=B1) and produce the list I have in mind. Currently I have to do some PERL witchcraft to get what I want, but I think this might be a common enough task to add as a permanent feature.
Now if you would make a classify.sharedotu(groups=A1-B1) command that would just be PHENOMENALLY handy 
Robin