It is difficult to say what direction the plot will go in if the game is in fact centered around Giratina. It appears as though there are three dimensions:
Beginning Dimension: Where Arceus exists and Dialga and Palkia came from. This dimension seems to involve the creation of life and the universe.
Existing Dimension: A dimension where life exists. This is where the storyline takes place.
Alternate (Ending) Dimension: A dimension where life ends and both people and Pokémon becomes spirit forms after death. This is what Giratina seems to be in control over.
If Giratina is the legendary Pokémon in the 3rd game, if the game exists, it will be interesting to see where the plot goes. If Team Galactic are the main antagonists in this game, what will happen? Will they somehow try to control Giratina to gain control over another dimension and somehow use the power contained in it to their advantage? Or will Giratina somehow play a role in defeating Team Galactic much like Rayquaza in Emerald? Cyrus obtained the legendary trio in order to extract the red crystals from their heads to form the Red Chain to control Dialga and / or Palkia. Those crystals appear to have the ability to keep Dialga and Palkia in control; the trio used them to keep their power in check, where Cyrus wanted to use the power of the 3 crystals to control the two beasts for his own bidding, effectively double-crossing his own organization. I cannot infer if the crystals have any connection to Giratina at all.
Again, this is speculation at work. We cannot conclude that any of this is true, or even if a third game is in the works (which is still an extremely likely possibility).
Random note... wanna guess why Dialga and Palkia are so easy to catch? They have a catch rate of 30. Normal legendaries have a catch rate of 3. The catch rate of Dialga and Palkia are comparable to Snorlax in FrLg, even though Dialga and Palkia clearly have 680 base stat totals, and then some, considering they can be given unique items to make them more powerful like the Latis. (source of stat information:
Legendary Pokémon).
Hopefully, these points of information can allow us to possibly speculate more. It will be interesting to see how far off the mark we are if the game does in fact get created. If Giratina is not the leading Pokémon in this third game, my guess is that the legendary trio will be instead.