Shiny Pokemon, aside from the colour, are no different from normal Pokemon - their shininess does not affect their strength in any way. It did in Generation II, when IV's affected gender and shininess, but now IV's don't affect these at all.
As for Milotic, here's some ideas for movesets and EV spreads:
Milotic @ Leftovers
252 HP/252 SP.DEF/6 SP.ATK
Marvel Scale
Calm
- Surf
- Ice Beam/Dragon Pulse
- Recover
- Mirror Coat
Despite Milotic's huge SP.DEF stat, a lot of people will still try to kill it by Thunderbolting it to death - Mirror Coat will punish anyone foolish enough to try. Surf for STAB, Ice Beam will let you OHKO dragons like Salamence/Garchomp whereas Dragon Pulse probably won't, but Surf/Ice Beam leads to you getting walled by other Water-types. Recover to restore lost health.
Or, something like this:
Milotic @ Leftovers
252 HP/52 DEF/200 SP.DEF
Marvel Scale
Calm
- Surf
- Ice Beam/Dragon Pulse
- Rest
- Sleep Talk
Rest activates Marvel Scale whilst healing you, which will increase your Defense stat. Sleep Talk will let you attack whilst asleep, and the attack moves are pretty much the same.
How's that?