Just a quick thought I had - given that the Bird Trio appear at Sea Spirit's Den after roaming in XY, could it be feasible that the Dog Trio appear in Scorched Slab after roaming? Sea Spirit's Den seems to be a reference to Lugia, the Bird Trio's master. Scorched Slab would be a fitting place to reference Ho-oh, the Dog Trio's master, in retrospect.
It's really cool that Deoxys might be catchable in-game as well. There are so many event Pokemon now that it's going to be difficult for GF to distribute all of them within each generation, so little by little introducing them as in-game catches will reduce the load, especially considering that each generation is likely to introduce around 3 mythical Pokemon every time. Perhaps in Gen VII we can expect to see Darkrai and Shaymin catchable, too. Then Keldeo, Meloetta and Genesect in Gen VIII, etc. I expect that the likes of Mew, Celebi, Jirachi, Manaphy, Arsues and Victini will remain event Pokemon until the end of time, but I'd assume that the others would be fair game as the series ages.
As for locations, here's my predictions:
- One of Raikou/Suicune/Entei depending on the starter you pick. Initially roaming, after a certain amount of encounters they can be battled and captured at Scorched Slab.
- Lugia/Ho-oh (version exclusives) found in the sky when the Silver/Rainbow Wing is in the players bag
- Regi trio catchable in the same way and places as the originals
- Lati@s joins you at some point in the game, the other one is catchable with Eon Ticket on Southern Island.
- Kyoge/Groudon (VE) - catchable in the main storyline
- Rayquaza - episode delta
- Deoxys - episode delta/post-episode delta in an area accessible by soaring in the sky (or - the moon!)
- Uxie/Mesprit/Azelf - Encounter all three in a cave accessed by soaring. Once found, the three scatter about the region. Mesprit would be found at Mt. Pyre, Uxie would be found at Mossdeep City (just outside the Space Museum thing) and Azelf would be found at Sootopolis City (just outside Cave of Origin)
- Dialga/Palkia (VE) found in the sky when the Adamant/Lustrous Orb is in the players bag
- Heatran found by soaring to a part of Mt Chimney otherwise inaccessible
- Regiggas found at the Sealed Chamber (possibly in a new room) - can only be battled when all three members of the Regi trio are in the players party
- Giratina found in the sky when the Griseous Orb is in the players bag (to get the Griseous Orb the player must have both Dialga and Palkia and show them to the relevant NPC who gives it to you maybe)
- Cresselia catchable on an island available via soaring / roaming the sky
- Muskedeers catchable on individual islands accessible by soaring
- Tornadus/Thunderus (VE) found roaming the sky
- Reshiram/Zekrom found in the sky when the player has the White/Black Stone in their bag
- Landurus found on an island accessible by soaring. The player must have Tornadus and Thunderus in their party
- Kyurem (Is there a Grey Orb? I don't think there is. If there is/if one is made then the same method as Giratina but with the respective Pokemon and items, otherwise...) found on an island accessible by soaring when both Reshiram and Zekrom are in the player's party.
If it was set out like that, then someone who didn't have access to Bank, the Eon Ticket or trading and played one playthrough of the game would have access to 21 Legendary Pokemon out of a possible 31.