Although it is just a rumor, I would not at all be surprised if Latios, Latias and Mewtwo would be available. Much like Ruby and Sapphire, they could just make Latias and Latios exclusive to each version and roam the grasses of Kanto like Raikou and Entei do in Johto.
They put the three legendary Kanto birds in the Platinum version even though they were obtainable via FireRed and LeafGreen. Since those two games are not available anymore, they put them in Platinum so you can still get them. The same now goes for Groudon, Kyogre and Rayquaza in HeartGold and SoulSilver. And Lugia, Ho-Oh, Entei, Suicune and Raikou are in there off course. Regice, Regirock and Registeel are obtainable via an event in Platinum as well.
That leaves only three legendary pokémon that are not obtainable through events, that they could put in and those are exactly Mewtwo, Latios and Latias. I'm particularly positive about the latter two. As for Mewtwo, they could at least have a Wi-Fi event or something for it.
As for Kyogre and Groudon, I like the idea of Groudon being on Cinnabar and Kyogre on Seafoam, especially since those places are pretty bland otherwise (given they are they same as in the GBC version which seems likely to me). The theme fits with them and you'd have something different than just the volcano and Pokécenter in cinnabar and the gym battle cave in Seafoam. On the other hand, it seems likely they are in the same place, like in Ruby/Sapphire's Seafloor Cavern.
I have no idea where they will put Rayquaza, though. Most likely they will put some new area in the game for it.