You are right to identify the content black hole but it’s only a problem if you let it be one. The hole exists as it (rightly) shares its scaffolding with Groups. Time will fix that: the list of things you cannot do with a Groups SharePoint site template is rapidly reducing and in time you’ll be able to do all of the things you need to do to manage information and fix the rift.
So it goes that if information management is critical to your organisation you might want to only allow Teams (or Groups) in defined situations.
In Teams I think we are seeing the future face of SharePoint, with SharePoint sliding into the background — being the content warehouse and workhouse. The positioning of PowerApps and Flow goes to reinforce my opinion. I believe that PowerApps and Flow will not just replace Infopath, SharePoint Designer and workflows but it will replace views and other UI workloads in SharePoint.
The challenge for organisations is that this will happen too quickly.