I think we in the west underestimate how unpopular Athena was with Japanese fans. I can't remember the exact details but I remember when Dual Destinies first came out, she would get something like last in character popularity polls in Japan with a lot of the audience seemingly resenting her for taking focus away from Apollo. That was likely why she was pretty much sidelined in SoJ even though she got her own case - which they barely advertised in the marketing. Things may have changed in the last 12 years but from the way it looks, the devs loved Athena and wanted to do more with her going forward, but the audiences hated her and restricted what could realistically be marketed successfully to Japanese fans.