Well, it depends.
If you are planning on using Kyogre competitively:
Defininitely re-trade it. Shininess is purely cosmetic, and a Kyogre with good IVs and Nature beats a subpar Shiny Kyogre any day. It may be difficult to give up this beauty, but it's for the best. Also, think of how easy it will be to trade for another Kyogre.
If you're NOT using it competitively:
By all means, keep it. This is a rare find, and that person must have been desperate for an Yveltal. Shinies are definitely good for bragging rights, and fighting with them in-game is always fun. Consider yourself lucky.