Sequencing and Informatics Platforms
I have not tried any other platform than Illumina, so my experience is limited to that. Ion Torrent and PacBio both had noted issues initially, but those appear to quickly be going away. As such, I am more concerned with the post-sequence informatics pipeline processing as a source of error than I am about the particular type of sequencing that was done. As for bioinformatics platform preference, I have done most of my work with Nhu Nguyen, Lauren Cline, and Zewei Song in QIIME. That said, I think that MOTHUR provides some great tools and can often be equally effective at analyzing the data (Pat Schloss has a great blog post about MOTHUR v. QIIME). The main hang up with MOTHUR for ITS based data is the creating the pair-wise distance matrix as part of the clustering process is computationally exhausting, so I have preferred the faster approaches used in QIIME. Along with QIIME and MOTHUR, many other similar informatics pipelines are in the works by individual groups and labs - Zewei Song has just published the FAST pipeline on GitHub (which is completely format friendly with QIIME), I saw at MSA that Jon Palmer and others at UW Madison have a new pipeline that incorporates mock community analysis (it is called amptk).