In the beta phase back in 2018 or 2019 I suggested its interface would confuse users. It does. You can't see what layer is turned on. Bring back checkboxes that are always visible; allow ctrl or shift clicking, and add a partial state checkbox symbol for Groups with only some layers in the group visible. The API stretching back to late 2x or early 3x has understood this stuff and AGS JS TOC could do it. It is simple HTML CSS.
Tooltip and different styling to tell users to zoom in for scale dependent layers. Like I added on www.sagis.org/map And replace the word Extent and Scale with 'zoom in to see map layers' and 'zoom to previous map area' and this kind of plain language. Bonus points would be a badge showing if a Def query was active and perhaps even allowing end users to turn it on/off and customize it (linking to the query widget to open that from the layer list via a little icon) we've all been there done that, and forgotten we had a def query active.
WAB was discoverable and intuitive. Also I suggest adding more color to icons in buttons, and make the Developer interface more like WAB. I hear this is coming, an Express mode. I've tried using ExB a few times and between lack of feature parity and complexity in developing I rever to WAB always. This divide is more marked than ArcMap-> Pro where by now, it might take a little longer to do something in Pro but at least you can do it (it has mostly caught up in feature parity)