We are using the Web App Builder (currently using v2.4) to create an application that shows two different maps side by side, with some custom functionality to link places in both maps. It doesn't seem like this is natively supported however, so I was wondering if anyone has worked on something similar, and if the Web App Builder is the right tool for this job or if we have to move to another ArcGIS product.
You might take a look at the Compare Analysis configurable app template and see if it meets your needs.
WAB does not have a side by side map theme. So you would have to do a lot of custom development to achieve this. AGOL does have to templates for this though:
Compare Two Web Maps, Side by Side
You can do this by creating a custom widget.
In this widget's setting page, you can config the map that you want to show side with the main map. In the widget, you can access the main map and the map configured for this widget, so you can sync the state of the 2 maps, like sync extent.
For the side by side view, you can use the dashboard theme to create a layout and then add the widget to show side with the map.