At the current state of things (Nov 2017), the pattern of site templates in SharePoint Online seems to be forgotten. Workflow replacement Microsoft Flow as well as all the other Azure services such as logic apps are very promising, but they are decoupled from SharePoint in a critical way. InfoPath replacement PowerApps suffers a similar problem. Previously, a site template for a specific reusable organizational structure was a good pattern to encapsulate documents and data around a single concept. For example, a project site template might contain template documents, predefined lists/libraries, and complex workflows that assist in the management and organization of a project.
With there being no way to "attach" these modern workflow systems to templates, it is impossible to package these units of organizations, which makes them essentially worthless tools.
My specific question then: is there some pattern or plan on how to achieve the same sort of organization that templated subsites provides, but fits in the modern evolution of the platform?
Perhaps there is a current way to link flows to site templates, but right now the status on that "issue" has been in limbo for months, with no official word as to when or if it may be supported. The only solutions I can think of is using the "native" SharePoint Designer workflows, but this is clearly not a good bet for long term viability.