The question I have is rather whether Relay is an alternative to Flux or that the two are meant to be used in conjunction. Also, which usecases would make Flux better and which Relay (if they are not to be used together).
Relay is one specific implementation of the Flux pattern.
Flux is a generalized pattern and there are a number of libraries out there which implement their own flavor of Flux. Relay is one of those libraries implementing the Flux pattern which focuses on describing data dependencies in the same place the data is used.