Although Arceus has the highest base-stat total, it is not perfect, even though it gets a super-boost from a plate on it, with a perma-STAB Judgement, it can still be defeated.
I would say Darkrai is the best.
With perfect stats, Timid Nature, 252 Special Attack/252 Speed EVs, and the Wise Glasses, it can be the best.
It's moveset would have to be Dark Void, Nasty Plot, Dark Pulse, and Ice Beam.
Starting off with Dark Void could make the opponent fall asleep, although with a semi-low accuracy, it may be better for Darkrai to be holding the Wide Lens. After making the opponent fall asleep, not only will you have an open target, but Darkrai's ability will begin to tear down the opponent. On the 2nd turn, use Nasty Plot, to increase it's Special Attack a great amount. Now, you can use either Dark Pulse or Ice Beam. Ice Beam is for good coverage, and Dark Pulse is good for STAB. And every time you use Dark Void, you have another chance at Nasty Plot. Once it's stats are maxed out, you are assured victory, as long as Darkrai cannot be outsped and cannot be hit by a super effective move.