Well... um... I think... Yeah, I have no idea what to think. Keeping my speculation tone downed, here are the options I see:
Placeholder: Well let's first address this. Yes, Pokemon has made placeholders before like Amethyst and WaterBlue, but these actually have logos (and nicely designed ones). Also I don't recall GF or the Pokemon Company having trademarked unused titles after Gen III since their naming conventions have moved onto something more random (at least that's what I always assumed that's why they did it, to assure someone didn't trademark/copyright the title before them though they'd probably be able to overturn that trademark if they really wanted to use that name)(EDIT: Apparently they did trademark "Gray" for Gen V and "Delta Emerald" for ORAS. Still though I don't think they would have too much problem convincing a court for someone to release a trademark that has "Pokemon" in the name. Say, did they ever trademark "Z"?). Like maybe a handful of people thought "Sun & Moon" and plenty of other games have used that relation before, but from a series who usually named themselves after colors and recently letters was anyone expecting Pokemon to use the pair it would be worth trademarking ahead of time? Plus with some additional "hints" like Masuda tweeting a picture of the moon this doesn't seem like a placeholder. But if it isn't, than what is it?
However I do want to note something about the titles. Look next to the "N" in "Pokemon" for the logos. There seems to be this random extra piece sticking out for some reason. The border follows the words perfectly fine everywhere else, just there both logos has something additional there.
XY2: Okay, so what in the world does the Sun & Moon have to do with the themes of XY? XY's theme is life and death destruction with Zygarde playing the role of balancing these forces. So where does the Sun & Moon come in? Well, philosophically speaking, one could try relating them to Yveltal and Xerneas. Sun & Moon can be used as a metaphor of begining and ending (Sun marks beginning of day, Moon marks end of the day. Xerneas can begin life, Yveltal ends life. Alpha & Omega). Or you could relate their colors to the Mortality Duo: Sun for Yveltal as its red and flies high in the sky while Moon for Xerneas since its blue and Fairy-types have a relation to the moon.
BUT the third won't really be about them, would it? It would or should be about Zygarde. And we know from the anime that Perfect Zygarde is made up of two cores, a red and blue one. Could it be that's where the relation lies? In many of the episodes we do see the Zygarde Core that's with Ash & co. (the red one) absorbing sunlight to energize itself while also looking up at the moon at night (and seemingly able to connect with the surrounding Zygarde Cells while doing so). We haven't really seen much of the Blue Core in the anime (it got captured by Team Flare as of a recent episode and that was during the day) so we don't know what its behavior is like towards the sun and moon. And yes, it's a loose string to hang on and could just be something the animators made up/are being artsy, but hey, who really knows what the anime team was told about Zygarde. So, yeah, maybe they decided forgo the obvious third version/sequel version idea (which they said they were going to do) and instead decided to make sort of standalone games so they could focus on Zygarde.
Gen VII: Then again, if the games were still going to be connected to Kalos than why not just make the connection obvious? Titles like these imply a new generation and those who may hear the title first but not know any background info might get excited as this does sound like a new generation. If these games were to be connected to XY it should be made obvious in the titles for marketing purposes. People who like XY would like a third version/sequel so titles hinting at one would get those people excited, how are they to know that these two new random sounding games are actually connected to Gen VI? But if they are, people who think this is a new generation since we've all been training to expect such naming conventions means new generation would be disappointed to find out these are just Gen VI games, moreso for those who didn't like Gen VI and wants to move on.
Thus, it makes more sense for these games be for the next gen, Gen VII. They've already showed us a new mythical Pokemon, Magearna, and if its going to be in the game it obviously won't be backwards compatible with XY & ORAS so they might as well go to the next generation.
"But... but... what about Zygarde and the loose plot strands"? Well first off this wouldn't be the first time there was loose plot strands left unanswered, I mean it was nice BW2 tied up some of its from BW but Team Flare was already an odd group that leaving some mysterious behind for them seems appropriate. As for Zygarde, well the disaster in XY was adverted so Zygarde didn't need to go Perfect. That's not the case in the anime, thus why Zygarde will need to go Perfect. So if anything Perfect Zygarde was sort of meant to be an anime thing, something to keep the anime's plot moving along until the release of the next games so they could ship Ash to Gen VII's region. Yes, they'll probably put Perfect Zygarde probably will be the new games, but it won't be the focus. It would sort of be like if Kyurem's original form was to released now, people want to see and use it but since we're not in Unova it won't have a role in the story.
Gen 6.5: I'm not really going to speculate much here since such an idea has never been done before so I have no idea what to expect. Like what would they do with titles like this? Pull a Johto and have a region right next to Kalos? Well, actually, we did say Magearna looked like it could be a Legendary for an England region and England is just a swim away from France... But back on track. I suppose if they did that I guess they could still do something with Zygarde while also having new Pokemon and maybe Legendaries. But if so Gen VI would be a pretty weird gen and it'll have so limited backwards compatibility it might as well be a new gen.
In the end, I think tomorrow's Pokemon Direct will explain all.
