The release of QIIME 2 2017.9 includes improvements based on the issues encountered in this thread: when loading TSV-based metadata, QIIME 2 now strips out any rows made entirely of whitespace. As well, the error message raised by QIIME 2 when it has a hard time parsing TSV data has been improved so that it is a bit more concise, and has more specific help text on how to fix the problems observed. Thanks! 