Business rules and Script Includes are still a bit more flexible, since you can create scripts of arbitrary complexity in Scripts Includes (this is offset somewhat by the possibility to use script steps in flows).. Flow Designer flows are more maintainable, since they are more structured.
Flows created by Flow Designer are more comparable to "legacy" Workflows and are meant to replace these. There is a bit of overhead in creating and calling a flow compared to a business rule, but they also have the big advantage that you can later go back at an execution context and inspect what happened in a particular flow execution - this provides some good auditing possibilities that you don't have with business rules.
I don't think we have hard and clear rules on where flows are appropriate compared to business rules, but my philosophy is that wherever there is a longer running piece of business logic that doesn't directly have to interact with the user interface, try using the flow designer. (If for example you are just setting a single field outside the context of a larger flow, a simple business rule is probably better).
