Not each independent feature — you can get this info from a feature table and plot in python, R, etc.
Sure. We don't have CSS or TSS (this is still an open issue and contributions are very welcome ) but for a rarefaction-free method you can check out q2-deicode in the QIIME 2 library: https://library.qiime2.org
Robust Aitchison PCA Beta Diversity with DEICODE
The main reason would be to preserve your entire workflow in provenance, so that someone (you, a collaborator, you in 5 years, etc) can figure out the entire workflow used to generate any QIIME 2 output. But functionally speaking no QIIME 2 does not do anything special during demux that qiime 1 did not do. I suppose the other reason is that you can get support on this forum if you run into trouble but qiime 1 is no longer officially supported (though the qiime 1 forum still exists). Speaking of which...
We don't have any official tutorials but there's a good deal of past Q+A on this forum that may be a good place to figure it all out. And of course you can always just ask to see if anyone know
In a sense yes — but denoising also filters out (and in the case of dada2 attempts to correct) errors in the reads.
denoise first. The denoisers in QIIME 2 have chimera checking built in, so you do not need to.
tabulate
can actually operate on all sorts of QIIME 2 artifacts (as well as TSV metadata files) because many QIIME 2 artifacts can be read as metadata. Have fun with that method
I hope that all helps!