Arceus is already an event pokemon as it is from what I know. Nintendo just needs to release an event we can get the Azure Flute from. Most likely the third legendary will be Darkrai or Giratina storywise.
Giratina: Each of the dragon trio rule over a certain portion of existance (Dialga is a ruler of time, Palkia is a ruler of space, and Giratina is a ruler of a portion of the realm of Chaos or w/e IIRC). Plus, if you observed the third in each series, it always seems to be one people never cared about. Pikachu was the third in America, and we thought it'd be Venasaur or something. In Crystal it was Suicune (but what else was there?), and Emerald has Rayquaza.
Darkrai: There is a possibility the storyline can be dramatically changed, so you might actually go to that city with the two towers of space and time (as an end storyline type of event, where the two beasts of space and time are released and clash. Darkrai, a rebellous type, fights the two to protect it's home and keep the humans from gaining too much power) where you can eventually catch Darkrai. It happened in Crystal and somewhat in Emerald and Yellow, so why not in the 3rd one?
Still, I'd rather see a Johto remake with a Pal Park and areas where you can find 3rd and 4th gen pokemon (Possibly a populated Orre region?) for the DS.