Subseeding is there to keep Skymin in the game while dishing out hits. With Serene Grace as the ability, it increases the chances of Air Slash flinching or Seed Flare lowering special defense. Take advantage of that and Seed Flare's increased accuracy with Wide Lens, and it already looks pretty nice. Max Special Attack for power and Speed, to get the hits in first. It's simple.

Seed Flare doesn't have really horrible accuracy, so Wide Lens can be replaced with Leftovers or Life Orb. Life Orb would sorta put a dent in the subseeding, but the Leech Seed does prevent Shaymin from losing HP, and the Life Orb adds power. Leftovers just helps it gain more, for when the Substitute breaks.