Damon, I'm sorry this experience has been frustrating. As has previously been mentioned, we strive to make our apps as simple to use and as engaging as possible for the most number of individuals. Because of this we unfortunately cannot meet every specific use case while still keep a clean, easy to configure app but we work hard to meet as many as possible. Through much of our testing, we have found that users who are new to online maps or just unfamiliar with a specific find it very confusing when they are presented with a list map layers to toggle on/off. There tends to be no context for the user to know why one layer is more important than another or how it relates with the rest of the layers in the map. For this reason we have designed our apps to always give context to the user before layers are turn on/off such as providing narrative context with map actions in the Map Journal or changing subject with tabs in our Map Series. We believe that adding this context helps the audience of a story quickly and easily understand the major "take-aways" of the story.
That being said, we understand that this structure is not ideal for every situation, especially when presenting your story to a more professional audience, to subject experts, or when more exploration of a topic is required. For your case, you may be able to use one of the two following scenarios:
1. Customize the app code to add a layer toggle
All of our apps are open source Github. You can find links to the code by clicking the "learn more" button next to the app of your choice on our app's list page then scroll down to the "Developer" section. The ArcGIS API for JavaScript already has an available widget that would allow a JavaScript developer to add the component with only a couple lines of code.
Pros:
- Faster loading experience
- Best integration as CSS can be added to the widget to make the look and feel match the rest of the app
- Better mobile experience
Cons:
- Requires a developer
- Requires you to host the final code
2. Embed the Web App builder in the Map Series
Both our Map Series app and Map Journal app allows you to choose what type of content you want in the main content area. This can be web maps from ArcGIS Online, photos, videos, or embed websites. Because the Web App Builder is just a web site, you can just embed it within the Map Series. Anytime you need a different map with a different set of layer toggles, publish that out as a new Web App Builder then embed it's URL into the story map. Here's a blog that explains how to embed apps within story maps: Embedding a Story Map within a Story Map | ArcGIS Blog.
Pros:
- Everything can remain hosted on ArcGIS Online, no need to download anything.
- No developer is required.
Cons:
- Sections that have apps embedded tend to load a little slower and may not work as well on mobile
- May not be able to match app styles exactly.
Hope this helps.