At first I wasn't sure about Articles not showing up in the tree also, but it totally makes sense.
Absolutely agree. Articles should not be in the Tree. Children that are not Articles, should show up, however.
Ok so this Multiple Article Containers idea is a big idea and considering you can achieve most of this manually with getResources and other addons for pagination, maybe it's not necessary.
I disagree entirely. Its very necessary. My site has over 15 Articles Containers (most are nested in other Article Containers) and grows with each user, project or development team that is created (moreover, it is all done on demand). It works extremely well, once you get the initial setup. You could achieve it with getResources, your own scripts, etc. But you could also write an entire 500 page novel bit for bit in assembler.
Articles already supports multiple Containers. It even supports nesting them, it just doesn't tell you that it does. In order to fix it, I spent about 3 hours searching the code, database, etc. All in all, after adjusting Articles on my site, it takes 5 lines of code to allow all of that functionality without losing any of the benefits that Articles gives anyway. Just my opinion, as my needs are vastly different from everyone else's.
It seems that Articles only supports tags within each Article Container
Actually, Tags use tagLister, so it has all of the support tagLister has. You can either a) adjust the call to use a different parent or depth, b) make your own tagLister call, or c) Nest Containers for an even better distribution of statistics (Articles supports nesting, it just doesn't tell you it supports it).
...modifying [Quip] email templates requires modifying plugin files...
You can do this by modifying the lexicon options. They are in Lexicon -> quip -> emails. No adjustment to plugin files at all.
Multiple Article Container pages
Supports this, see above. Additional modification may be required for
expected and desired behavior. I think this depends on what you want it to do with Multiple Containers.