When sharing a web layer from ArcGIS Pro using the ribbon (Share > Web Layer > Publish Web Layer), there should be an option to share the layers from your map separately (split out) instead of grouping them all together into one feature layer. Currently, you have to right click each layer and share each one individually if you want separate feature layers.
This way, when you add content to a web map on AGOL, you can pick and choose the individual layers instead of having to add all layers from the published feature layer (then having to delete the ones you don't need).
This could either be set up on the Share As Web Layer - General Tab or Content Tab.
See screenshot of mock-up.