I’m in a similar situation, actually. There aren’t a lot of great options. I use DEVONthink and iA Writer at the moment—the former for browsing, the latter for writing.
There is a really neat app that seems to be abandonware but fits your use case: Outlinely. It works pretty well, save for a few bugs, but I could never adopt it because of the looming feeling of dreadful abandon.
There’s a v3 of DTtG in the works. Suffice it to say that I have high hopes!
Same here! They snagged the look and feel of Dynalist.io, which isn’t a bad thing, at a better price. But aside from a small flurry of updates in the summer of 2018 the app really hasn’t been updated.
It has a lot of potential as an outliner but I’m not sure I’d want to use it to do any longer-form writing, and it’s not really optimal as a personal wiki. .If you’re willing to get geeky there’s open source options like MediaWiki and TiddlyWiki.
They do have embeds, but it’s limited.
Have you looked at Scrivener? I used it only shortly, so I do not have deep knowledge on it, but it is a very powerful app.
Unfortunately scrivener document links only work on the Mac.
Thank you for all the replies!
Regarding the use of a second iPad, I like the quickness of the software and its “limitations” (focused UX). I also use a lot of shortcuts to jump to certain things that I need on the fly.
Regarding the “hard questions,” it is not necessarily hard. For example, if someone asks me how the CIA involved itself in the politics of Latin America, I could go on for hours about the macro- to meso-level, but I want the ability to point out specific actors, players, dates, etc. I would absolutely respond with an “I don’t know, but I will get back to you on that.” But the problem I have is not necessarily a lock of overall knowledge, but a lack of what I would think are easy. Another example might be if a student asks about the death toll in World War II for some specific nation or for civilians, or potentially wounded but not killed. I can describe this in broad terms, down to a respectable rounding error in most cases, but I want to be able to make a few quick taps and get the data.
I am definitely on the geeky-side, but maybe not to that level. I have built web pages and have worked with publishing languages, but nothing extreme.
Another thing that I forgot to mention is that I do really desire to remain plain text, and potentially local for all my notes. All the suggestions are wonderful! Thank you.
I found Hook via this other thread.
Then Hook’s forum led me to another new (web) app:
@Robertson.historian et al., you might want to explore these options. They’re now on my list!
I think it looks great, but it is macOS only right? I am iOS first, and Mac 2nd.
Hook is macOS only, yes. Sadly!
You’re going to think I’m nuts, but you might want to try Working Copy. Yes, it’s a Git client, which is a type of version control, but hear me out.
It has markdown, it has search, you can link to other files in the repository media files as well as markdown files, I haven’t tried PDF or images but they should work.
You wouldn’t have to get too serious about versions and stuff if you didn’t want to, although I’m currently experimenting with using this as my main notes location, and finding it pretty good. It integrates well with the Files app, and you can edit files in place with another app, if you don’t like the built in editor.
Not yet. Roam’s web app-ness has kept me away for now.
On Hook, though: your question prompted me to buy a license with Hook’s Black Friday sale. I haven’t installed it yet, but I did some exploring of the forum—and oh wow this is a great thread that you’ll probably truly enjoy. It seems like Hook’s on a great path.
Though it’ll likely be a while, I’ll make a note to post back here when I have the chance to play with it.
Damn it, I forgot to buy Hook on Black Friday 
I purchased Hook yesterday, too.
I’m also frustrated by the webappiness of Roam, but I read that they’ve got plans for desktop versions and want to figure out how to think with it in the meantime.
Will respond to the Mesh thread in a bit, after I’ve had the chance to read it.
Some followup: Roam actually works quick well in an iOS browser, and frankly really well if not indistinguishable in the iPadOS browser. Experimenting now. Should be a revolutionary piece of software.
How does the pricing work for Roam? Had a quick look - seems quite interesting.
Currently free since it is in beta. It will be a subscription service in the future from what I understand.
Just preemptively posting this. 
Great way to kill an interesting-looking piece of software.
I am not as anti-subscription as most, it just depends on the pace of development and the feature set. I do like the old model from the 80s and 90s, but in this marketplace I don’t think it is in the cards to have that model dominate. As has been mentioned on this forum a lot, the Agenda model is nice (it basically models the 80s and 90s model). But I have no problem spending a $30-40/y on a critical piece of software - and to support the developer.
I understand your position. But I am tired of all the subscriptions and developers trying to maximise their profit in any way possible. Unless you are not providing a continuous service (with connected costs), a subscription is not justified (in my opinion). Unless I absolutely need an app, a subscription is a deal breaker for me. I want to buy an app and not rent it. If the developer wants my money, he can make a new version with good new features and I will buy it. That being said, I like the compromise Agenda has (as you mentioned). Hopefully, that will be the way to go.