In the last couple of years, my preferred BLAST output format has switched from BLAST XML to plain tabular output. The main reason for this it is easier to parse, and now gives easy access to more fields - BLAST+ 2.2.28 added descriptions and taxonomy output to the tabular and CSV output, but the cumulative effect is BLAST XML has been lagging behind.
However, there is a simple change the NCBI could make to greatly improve the usability of the tabular or CSV output - label the columns with a header line! This is vital meta-data: No-one should be forced to guess-the-columns when presented with a data file.
