So I realized a few things about Giratina.

I want to start with it's origin.
As we all know, Giratina is based off the basilisk, a slow venomous lizard that is only
defeaated by it's own reflection. Knowing that Giratina lives in a world parallel to ours,
It wouldn't be unheard of if Giratina had this same weakness. In fact, the anime depicted
that it could only get through to the other world by passing through reflective surfaces, e.g. water, mirrors.
But then, I started thing about it's typing. Dragon/Ghost is pretty odd; being weak to your own type
not once but twice is unique. Maybe it really is weak to itself.

Then I realized it had two forms.
These forms live on opposite poles of the mirror, so to speak.
It's Defenses also switch with it's Attacking stats. Ones a wall. The Other an Attacker.
Both were made to break the other. One the "Origin"al. The Other has been "Altered".
Giratina is also meant to represent Antimatter, a substance that when collided with our matter generates massive energy.
Maybe that could be interpreted as a Super-Effective hit.

The Basilisk has two distinct interpretations on it's appearance.
One is that of a Serpent, like in Harry Potter.
The other a Six legged Lizard, like in Dungeons and dragons.
Also, Their cries are the same, unlike shaymin.

What about Shadow Force?
Shadow force make the opponent disappear right, but the are still susceptible to weather.
That's because it's still there just on it's plane of existance. It can't be blocked because it attacks the foe's "reflection"or the
plane the foe was not aware of.

The both have 6 legs, 6 golden ribs, and 6 black and red appendages
6 split between 2
6/2=3
Half Life 3 confirmed
Oh wait, Antimatter has no half life.