Well apparently Arceus is the third part of the them, according to Bulbapedia. But he's an event Pokemon so it won't be him on the Box Art. It'll more than likely be centred around Giratina.
As far as we know.
Think about it this way.
Arceus was born from the Cosmic Egg, as the library states and we know he emanated forth Dialga (Time) and Palkia (Space) both aspects of his own power, and from his body created the lives called Uxie, Mesprit and Azelf who more or less fabricated the "conscious" universe (Uxie is Knowledge, Mesprit is Emotion, Azelf is Will).
Then once the universe was in place Arceus withdrew to the Place of Origin and went to sleep.
The story never describes a third aspect but if anyone we've met is it it's Giratina. Giratina has a face like Palkia and Dialga's, he's half Dragon and he has a similar move pool. The thing is that I'm just...not sure what Giratina's role is. My best guess is that he is some sort of self-appointed deity of the Void who doesn't take any role in creation and resents his brothers. After all, he's the Renegade, and he seems to dislike humanity, choosing to spend most of his time in a far away dimension and emerging every spring into the necrohol at Turnback, when it's shrouded in mist. Maybe he's a failsafe of some kind?
Interesting...but they seem to talk about Giratina in that area as if its the controller of death, and not even related to Dialga/Palkia...well, while it IS obvious that Giratina would be the star of the third game (unless they pull a Crystal and make it Mesprit), I don't think it actually belongs with Dialga or Palkia. I think it's more of the anti-Arceus, in a similar vein to the Kyogre/Groudon rivalry back in R/S/E. After all, death is the opposite of life, and they talk about Giratina & Arceus in those respects, so...
Anyway, um...yes, it would be nice to get a G/S remake...but if it happens it won't be for a while, so we will be speculating for some time more.
Sure, in Shinnoh there are plenty of references to Johto, but there are plenty to Hoenn as well. Jasmine is in Sunyshore, and a nameless Hoenner is in Heathome. The guy you trade shards with for TMs is from the Weather Institute from Hoenn. There are probably others, and although I must admit the Johto cameos are most prominent, there are plenty of them for Hoenn as well.
Death is opposite life which, really, started with Mew as the first basic non-deity or with Uxie, Mesprit and Azelf as actual Life. It is NOT, however, opposite Existence. Arceus created the Universe through its Emanations and its children. Dialga and Palkia are Matter and the children are Consciousness (I said all this already). So Giratina is probably less an Anti-Arceus than an anti-Matter (the Void), thus standing against Palkia and Dialga. ...That probably made no sense.