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Re: bat origins - the smoking gun: guidelines

Well -- those guidelines are guidelines for conducting a phylogenetic analysis. Nothing wrong with them. Except that I don't think anyone of us has the time to compile a phylogenetic analysis of Placentalia right now. So I don't quite understand what your point is.

I say 'taxon selection is everything', but that is really true only
after a certain minimum number of characters are employed from every
corner of the body,  I found that 150 will get you 95% there and 225
will provide well.

Depends on the number of taxa. To choose really trivial examples, you most probably won't need 150 characters to resolve a tree with three taxa, while 150 characters are incapable of resolving a tree with 1000 taxa.

3. Avoid suprageneric taxa like the plague.

Molecular data matrices are almost always completely devoid of them. OTUs in molecular matrices are by default specimens.

The study of the ancestry of bats has suffered from all of the above.

I disagree. The latest molecular studies (of the last few years) have very broad and ever-increasing taxon samples, large and ever-increasing numbers of characters (the latest JVP contains one with 22 genes!), and have specimens as OTUs.