Hi @Willis! These are all great ideas, thanks for sharing them with us! I was planning to tackle some of this for the upcoming 2017.12 release, but ran out of time. Hopefully we will implement these ideas in early 2018, though I can't provide specific time estimates. We'll follow up here as progress is made!
We have some open issues tracking these ideas, and I've cross-referenced your forum post on those issues. Specifically:
The Moving Pictures tutorial aims to provide an end-to-end "general" microbiome analysis, but a wizard/flowchart/roadmap would be a nice complement to the tutorials. We have an open issue tracking progress on that.
We have a spreadsheet that's incomplete and in need of some cleanup, with open issues (1, 2) to fix that and turn it into proper documentation.
This one doesn't have an associated issue. Our recommendation is for plugin developers to write tutorials covering whatever is relevant to their plugin (e.g. theory, example data, usage). Plugin developers can add their tutorials to the forum's Community Tutorials (there are already several there!), or host the docs wherever they want to. Community Tutorials may be transitioned into "official" tutorials (i.e. hosted on https://docs.qiime2.org), but either location is a good spot to look for details about plugins, what they do, and how to use them.
Are there specific topics and/or plugins that you think would benefit from the expanded docs you described? That'll help us prioritize what gets documented.
Also, the type of info you're requesting may exist in some of the tutorials already (the Moving Pictures tutorial includes some explanation about why you'd perform certain analyses, though it's certainly not complete). There's a new community tutorial on alpha/beta diversity analyses that may be interesting to you as well.
Thanks for the feedback, we appreciate it! Happy QIIMEing! 