Hi @balford, and others...
I've uploaded, what I consider a "first-pass" on trying to fix the SILVA taxonomy issues. Particularly those of the Eukaryotes. I've uploaded files on GitHub, for the community to test and play around with. The classifiers, and the files used to make them, are available there.
Right now I'll update the documentation as I have time, things are quite busy at the moment. 
Let us know if this is useful. We are working on a more streamlined and cleaner approach to provide these. But I figured I'd pass along this short-term quick-fix for those in need.
Cheers and happy :qiime2:-ing!
Mike