Hmm... So we have:
Uxie
Metagross
Mewtwo
Alakazam
Arceus
And Meowth is kinda out of it in terms of raw intelligence.
I think that it's possible that Arceus isn't all knowing, because it's only stated to be a creation deity, who seems to have taken to long naps in artificial galaxies and glass palaces since then.
So, it seems, it comes down to this. Is a being with an extreme IQ more intelligent than a supercomputer? Supercomputers can, due to electrical circuits, process information extremely quickly, but can only perform actions that have already been programmed, or "learned". IQ measures information which has been programmed and recalled. Mewtwo has been seen recalling information which has not been gained through experience, and it seems likely that it's a trait gained from Alakazam. So, it's possible that Metagross is a faster thinker and recaller, while Mewtwo and Alakazam, who share DNA and possess a vast amount of hereditary information, are more intelligent.
I realize I have entirely overlooked Uxie, but that's because I'm not exactly sure what to make of him yet.