I've got an idea that might work. Have normal legendaries work as they do in the handhelds, but have shiny legendaries use the current system, with guaranteed good IVs.
Personally, I use legendaries as a sort of badge post E4, and I also use them in friendly matches every now and then, but there being only one on the server really kills that.
Edit: Maybe as an incentive for holding onto shiny legendaries, have them double exp gain or egg hatching rate while in the party? Though, it'd be pretty unsafe having eggs in a party when everyone's trying to take the legendary from you.