I'm going to dump common confusion and requests that I see with accounts I interact with in here. I figure that since I often deal with the least technical clients, it will provide a window into the less intuitive areas of vanilla. It also may provide more granular insight on issues that factor into Larger companies deciding that the software is to difficult to manage. I'll try and keep actual bugs out of here and make suggestions as I go along, I just need a dumping ground to organize my thoughts. I'll add to the OP as I go and remove things if they get filed to github.

Dashboard

Better Deletion/bulk action tools
In the spam queue, people really want to be able to empty that out despite the consequences of doing so without looking. I mentioned in Unassisted onboarding that I think we could the same selection tool we have on the forums we use for threads, as that would at least give you the flexibility to look at different pages and then delete. I would also suggest at the very least, some organization of that page. Can I look at all the spam that came in that month? Maybe simple search so I can see similar spam by keyword?

Roles and Permissions
Roles and permissions need better clarity, more than just the names of roles, people sometimes just don't understand what role has what permissions.

You can see how bad this is on a site like battle bears:
http://battlebears.vanillaforums.com/dashboard/role
Not only do they have 24ish roles, a bunch of them are similar in name. Are they actually different?

On the User page, searching the term "Administrator" or "Moderator" should pull up roles with these important permissions regardless of what they are renamed, or perhaps there should just be a separate list for admins, moderators, and community managers, so that the site owner (and us, in support) can more easily keep track of who has elevated permissions.

Spam
Not sure how to tackle this, but better indication that ranks/reactions/and flood control are involved in good spam prevention would help new people turn on those settings before they start getting flooded with spam and start back peddling, I would think a little blurb in the spam queue may help.

Notifications
Approval, Moderation and Banning Queue notifications for admins via email

Make it so you can't delete social groups
Or make it so it doesn't actually appear in the category page at all, It doesn't seem like the client needs to interact with it?

Client ability to toggle AutoConnect
Is there some reason they can't? The majority of clients think their SSO is broken if it hasn't been switched on for them

Turn off popups when forum is set to connect
This option is buried in the embed settings, but it helps with SSO implementation in general,
ex, StanwinstonSchool: https://support.vanillaforums.com/discussion/comment/19266/#Comment_19266

User Experience

Drafts
Option Remove all drafts.

Emoticons
Some of our whiney clients want the giant grid of emoticons back, complaining that auto complete requires too much remembering, still.

Best Of
Best of seems to be a bit broken. Heres a thread about issues on pebble:
https://support.vanillaforums.com/discussion/1976/re-bestof-page/p1

This thread is from april 2013, but if you look at their best of page right now http://forums.getpebble.com/bestof, you can see formatting issues still. But if they haven't reported it in since then, does that mean literally no one looks at that page?

Some things that might make it more interesting/useful:
*Organize by reaction (I think you can, via /bestof/awesome or bestof/reaction, but it's hard to tell if does anything)
*Display how many reactions something has on the page, to give a better indication of why it's there
*A few different time ranges (best of today, this week, all time)
*trending vs staff picks
*Expantion for long posts so you cant end up looking at a page that looks like This

I can mock up some interface ideas but I'm not sure what features are feasible.
tumblr (explore page)' tending and content types at the top, popular searches on the side (tags)
Pintrest (search results) Really nice simple options for filtering