Feraligatr's DPS with Hydro Cannon is nowhere near Kyogre because of waterfall, and actually Swampert and Empoleon will outrun it (Feraligatr) if they have Hydro Cannon and will actually go close to Kyogre. And that's assuming bubble is Empoleon's fast move.
Of course it's long talk but Greninja will outrun Kyogre in terms of dps with Hydro Cannon but by that time Kyogre will likely have a primal form.