For this discussion, we will mention a few facts;
-Currently Celebi with Hold Back, Blazikenite, Discount Coupon and Inkay with Happy Hour are released.
-The next movie's poll is featuring Darkrai, Victini and Celebi.
-Previous popularity polls generally featured Pokémon that were released again after the event, making the polls unimportant.
-Entei gained Sacred Fire, whereas Zapdos' Hidden Ability was changed to Static. Similarly, Cresselia got Moonblast and Genesect got Fell Stinger. Heatran and Genesect's signature moves were also tweaked.
-A major three or four month long event has been given in X/Y for two periods(Blazikenite and Discount Coupon).
-Jirachi is always released for at least one Tanabata event in Japan in each generation, regardless of other events.
-For three generations, the pixie of the two generation after was granted an animated appearance near the end of the generation and an event to go with it. This appearance might be a movie(Celebi in Movie 13, Mew in Movie 8) or a TV appearance(Jirachi in Best Wishes!). Next in the line are Manaphy and Shaymin(though the latter is extremely unlikely as it was never promoted as such).
-Most previous mascot legendaries are released for the later parts of the generation, with many of them being previously available through connectable spin-off titles than in-game locations.
-Miyamato has previously expressed his idea to bring back older titles, which seems to be true for Pokémon spin-offs as well, if Trozei is anything to go by.
-Serial Code events are available through X/Y. This opens up possibilities for repeats of the Pokédex Guide/Pokédex iOS Gothorita.
-If one were to assume that there will be another regional dex for the next game, and other regional dexes were given equal Pokémon, there can potentially be 8 more Pokémon, which would be sufficient for two trio masters and two trios. If the Coastal Dex gets increased to 154, then this number increases to 12, providing one more legendary and a trio.*
-For the purposes of this blog post, we will consider three scenearios;
Scenario 1) There are only two sets of games in Gen VI. Second game takes place in Kalos, partially or completely and provides an addition to the Regional Dex.
Scenario 2) There are three sets of games in Gen VI. Second is set in Kalos partially or completely and provides an addition to the Regional Dex. Third set is a remake of or sequel(s) to Ruby/Sapphire(with elements of Emerald) or spiritual successor to the Ruby/Sapphire/Emerald.
Scenario 3) There are three sets of games in Gen VI. Second is set in Kalos partially or completely, whereas the third is in another region.
Now we can start, case by case;
Zapdos/Articuno/Moltres with Hidden Abilities:
-In FireRed/LeafGreen, the Legendary Beast player encounters was chosen by the starter that was chosen. This method was repeated with the Legendary Birds in X/Y. However,the player could get the other beasts from Colosseum. It is likely that this will be repeated with the legendary birds in one form of promotion or the other. It is also possible that their Hidden Ability counterparts will be the versions that will encountered in the next game, which would provide extra incentive to get the previous iterations, X/Y. However, as the Gen I Legendaries' Hidden Abilities are superior to their base ones, and as most Hidden Abilities are made available through alternative encounter and obtaining method, this is not too likely.
The Lati twins have been released for the last games of their generation for two generations. Whenever they are released Soul Dew was available as an item, either through an event(for Gen III and IV) or in-game(Gen V). As their Mega Stones are likely created to replace Soul Dew as their event-only item, it is reasonable to expect that Soul Dew will continue to be available in-game in the games they are available in-game, or vice versa. However, if there is a set of Ruby/Sapphire remakes/sequels with Emerald's elements, it is likely that Eon Ticket event will be ressurected, which can potentially mean that the Mega Stones will be in-game while Soul Dew continues its original event-only tradition. This is not too likely, as whatever promotion Lati twins it will obviously be for the Mega Evolutions as Soul Dew was already used as a plot element in Movie 5, and by proxy the Mega Stones will be the event-only items. Of course, whenever the said remakes/sequels happen, the Lati twins will be released for that game.
Outside of this, there's no reason not to expect that they will continue their version exclusive with other one being available through event, especially if there are two sets of unique items for both parts of the duo.
Though it is not bound any real traditions, this event-only Pokémon was generally released for near-end of each generation. However, if there is a game with the Emerald's elements, it is likely that Aurora Ticket event will be revisited.
Entei/Raikou/Suicune/Ho-oh and their Hidden Ability counterparts:
As mentioned above, Entei recently gained a new move in its arsenal. As such it will likely be showcased in some manner in some event in the near future, in-game or otherwise. Similarly, the rest of the beasts will likely follow suit, as well as their master Ho-oh. However, as mentioned in the Legendary Birds' page, their HA version do not need to follow suit to their standard versions.
As Legendary Birds' den is called Sea Spirit's Den, it is not unlikely that the connection between Birds and Lugia will be properly canonized in games' universe. Of course, if Lugia were to appear in the Sea Spirit's Den, it would increase the maximum count for Coastal Dex to 154. Of course, if Ho-oh were to appear, Lugia would likely follow it, as it has been the case for most games except Colosseum and vice versa(except Lugia did appear in its sequel XD).
Not only they are French inspired legendaries, each one of them is associated with an element that is in abundance in Kalos. As such, it is reasonable to expect them in next Kalos game. As for Keldeo, it is reasonable expect it to follow others, even though its connection doesn't have to be that strong.
As previously mentioned above, Manaphy is one of the pixies that is next in the line for an end of generation appearance. However, unlike others Manaphy is also related to Rangers franchise. If it returns, one would expect Manaphy to be available as an event again. It is also possible that its animated appearance might be related to the Ranger game and its event, as it has been the case with previous Ranger specials(and Movie 9) and their releases.
As previously mentioned, the "duo" are one of the legendaries to currently gain new level up moves without appearing in X/Y. In addition, Heatran was previously mentioned in Jaune Plaza and Kalos has some volcanic activities that can provide a shoehorning for Heatran. As for Cresselia, it was never bound to anything outside of Fullmoon Island(which is still near Sinnoh) and Lunar Wing, as such it does not need to reason to be present.
Remaining Hoenn Legendaries and Regigigas:
As with previous remakes, these will be present in their original region and not elsewhere, however if there is no return to Hoenn, they can appear anywhere they want within Kalos or a new region. As for Regigigas, its last two games were in places where other Regis were accessible, so likely the future games will continue this idea.
As these two don't currently have any established pattern, no one can say anything about their appearances for certain. However, Darkrai is likely to appear when Cresselia appears, and both of these will be released sometime after the Xerneas/Yveltal movie's events' end.
Most commonly, the last game of each generation contains access to the mascot legendaries of the previous generation, with the exception of FireRed/LeafGreen/Colosseum. It is likely that the three will follow this route, though as both in Gen III and V the mascot legendaries were made available by external software, it is likely that the Tao Trio will be available within another spin-off title.
Arceus might appear within this generation to showcase its Fairy-type forme.
Other event legendaries are harder to predict either because they have no established pattern or are released too soon to be discussed. One logical assumption would be that events that weren't released in Gen V would take priority. However, only currently unmentioned and unreleased event legendary that wasn't released in Gen V is Mew.
The other trios have no contemporary significance, and lesser trios never had much significance in their releases. As such, we can't describe when Pixie trio, Creation trio or Kami trio will appear, but all three of them have some connection to something, Creation trio are connected to the creation myth of Pokéverse, Pixie trio are connected to Sinnoh and Kami trio are connected to Japanese style shrines.
So, for recap:
Hidden Ability counterparts: Near-future event for legendary birds, N/A date event for others.
Raikou/Suicune/Entei/Ho-oh: Possible appearance in the next game, possibly Kalos.
Lugia: Possible appearance in the next Kalos game.
Hoenn legendaries: Hoenn remakes, otherwise end of generation for Lati twins and N/A for the others.
Deoxys: End of generation event.
Jirachi: Tanabata event.
Mew: Possible near-future event.
Arceus: Possible near-future event.
Manaphy: End of generation event and animated appearance, possibly Ranger game.
Shaymin: Alternative end of generation event and animated appearance, otherwise N/A date event.
Cresselia/Heatran: Possible appearance in the next game, possibly Kalos.
Zekrom/Reshiram/Zekrom: Possibly end of generation, in-game or alternative software.
Darkrai/Victini: Later date event.
Everything else: N/A date. Event for event Pokémon, in-game appearance for Kami and Pixie trio. In-game or alternative software for creation trio.
As for alternative software possibilities, lets discuss them;
Currently running spin-off titles are:
Pokémon Rumble Series: Iwata himself mentioned that he will be working towards more NFC possibilities, whereas Rumble U already uses it. This reason, along with the decent sales of the series and relative low cost of production might push another sequel.
Pokémon Mystery Dungeon Series: As this series always had decent sales, it likely won't end.
Pokémon Trozei 2: Coming Soon.
Great Detective Pikachu: Also Coming Soon, but due to more mature nature of the game it likely won't feature any major event codes.
Previous titles that can return:
Ranger Series: As mentioned above.
PokéPark Series: There is currently no Wii U version of this title.
Stadium/Battle Revolution Series: Not too likely, as terrain moves render alternate fields useless, and current 3D graphics makes a 3D title moot, and HD models would be too much work for the developers.
Pokémon Conquest 2: Though it is hard to say that there will be ongoing event correlation between main titles and this title, it can be attempted.
Pokedex 3D Pro: Also useless due to 3D graphics.
Pokedex for iOS: Possible, but it would just be an update to the existing title rather than a new iteration.
Pokémon Snap: Possible, but also useless thanks to fact that photography is a major part of the X/Y.
Learn With Pokémon: As it is a teaching game, putting an extra incentive to purchase it would be outright villainous. So no.
Dash: Dead and buried.
On the second thought, we will probably see another one-off title like Dream Radar than this.
*Edit: On a very important note, I have not noticed that PokéBeach's screenshots and rumors have stated that Diancie, Hoopa and Volcanion are all in Central Kalos Pokédex, completing it to 153 Pokémon. This makes it much more likely that Mountain Dex will also be completed to 153, but it also means that one of the potential slots for a trio is already complete. This also potentially means that Lugia might not appear in Sea Spirit's Den, but rather a mountain area to keep the 153 number. Alternatively, other places can be increased to 154 except the central dex, as it won't be completed through convential means and it won't be complete until at least the second movie, and it is extremely unlikely that there will be more Pokémon from previous generations that take place after the last true event Pokémon of the generation(as it has been the case for previous National Dexes except for Manaphy and Victini, which were the first event legendaries of their generation).
Edit 2: The pics are on smealum's website, so it is legit. Here's Hoopa, Diancie and Volcanion.