Ho-Oh's wall pattern which were never explained, there was a sign of another Pokémon being involved from the get-go:
"The ruins are from about 1500 years ago. Nobody knows who built them. It's also not known if the Pokémon statues have any meaning. It's all one big mystery..."
"It's a replica of an ancient Pokémon."
"Our words shall remain here for the ages. Thus we shall erect a Pokémon statue outside."
The statue looks like Rhydon, but common sense dictates that a statue of unknown meaning doesn't actually depict a common Pokémon; Game Freak had to show us something, so they used a generic sprite. Now, I don't think the statue represents Arceus, either, because then it wouldn't stay a mystery in HGSS. Furthermore, the Sinjoh Ruins event gives us a good idea that the Ruins of Alph tribe only came to hear of Arceus after they had built the Ruins of Alph. Also note that there is a different kind of statues in the Sinjoh Ruins, suggesting that the tribe changed their vision of the relevant Pokémon.
There are three loose threads related to unknown Pokémon:
1) The statues
2) The GS Ball (which doesn't contain Celebi)
3) The fallen giants
Now, the statues may represent more than one Pokémon and the giants may actually be in singular form (as per the Japanese text). Personally, my theory is that these Pokémon are all one and the same, but I'm not going to go out of my way to prove that when we obviously don't have enough data.
I consider this to be a far more interesting mystery than anything pertaining to the Abyssal Ruins. Whether or not the story of the ruins is just a prophecy of Black and White's main plot, the king certainly comes very close to being the player character.