You mentioned some of them, but I'll post my theories based on various clues and bits of info. I'm warning you now that this will be a long post...
1) Okay, so it's known that GameFreak was one of the first companies to receive 3DS development kits from Nintendo. I believe Nintendo gave GameFreak the kits with a silent expectation of them to develop a main series Pokemon game on the 3DS soon. GameFreak seems to have been experimenting with it all these years through things like the Pokedex app.
However, GameFreak still released Black2/White2 on the DS more than a year after the 3DS was released. Notably, they included 3DS-exclusive content like the Kami Trio's Therian Formes and the Dream Radar. My theory is that these were only made to appease a Nintendo that was hesitant to allow anymore DS Pokemon games. Why do I think this? Because the coding of Black/White suggests that the Kami Trio (and Keldeo) were never planned to have new forms, while Kyurem was. There's something in Kyurem's data in those games that was also found on Rotom, Shaymin, and Giratina back in Diamond/Pearl, all of which got new forms in Platinum:
http://pokebeach.com/2012/02/placeholder-for-kyurem-forme-found-in-black-and-white-coding
That bit in Kyurem's data isn't found on the Kami Trio or Keldeo, suggesting that their new forms were both conceptualized and created in the middle of development on Black2/White2. If they felt the need to make previously-unplanned content just for the 3DS, it probably means that they can't get away with any more DS games.
2) That takes me to my thoughts on Ruby/Sapphire remakes. I don't see them being made for the DS due to what I outlined above, but being the next games on the 3DS is just as unlikely in my eyes. If GameFreak was experimenting with the 3DS capabilities for the main series all these years, I can't imagine their first main foray into the 3DS being a remake because the 3DS requires a complete overhaul of the graphics, sprites, backgrounds, etc. Why would they go through all that trouble for Gen 5 games? Especially when they would become obsolete the next year with the advent of Gen 6 games on the 3DS that wouldn't be fully compatible with them. It makes far more sense in every way to release Gen 6 games first, and then potentially use the 3DS look for remakes and retain full compatibility between them. Not to mention having the full impact of 3DS capabilities on top of 100+ new Pokemon by having Gen 6 games first.
3) My last reason lies within the upcoming Genesect movie. The title was recently revealed as "ExtremeSpeed Genesect," but it's strongly implied to be an abbreviated title. As Serebii reported it:
"The sixteenth movie has been revealed to feature a shiny Genesect, showcasing the appearance it has in flight, and be called Extremespeed Genesect, with tradition dictating there will likely be an addition to the title in the Spring."
The tradition he mentioned is something that they've been doing with the movies for a while now: withholding the full title and/or details of the movie until around the February before the movie's release. This has included new Pokemon or new forms, but Serebii confirmed that the flight appearance is not a new Genesect form since the names of forms are specified a certain way in Japanese and the way Genesect flies is not referred to in that manner.
Coming back to the title, "ExtremeSpeed Genesect," it's much too short for a Japanese movie title. It's extremely likely that they're withholding the full title of the movie since it reveals something big. The last time they did this was with the Zoroark movie, first called "Ruler of Illusions: Z." When Zoroark was revealed, the Z in the title was changed to Zoroark. If the Genesect movie's full title includes the name of a Gen 6 Pokemon, it's definitely not going to be of the Munchlax sort as some theorize, but rather an important Pokemon that might fill a protagonist role against an antagonistic Genesect. Such a Pokemon could also fill a speaking role for interactions with Ash and co. since Genesect seems like it might not be entirely speech-capable (being cybernetic and all).
So there you have it. These are my reasons for believing that Gen 6 is coming, and all the recent teasing and hinting by GameFreak higher-ups as well as blacked-out merchandise related to the Genesect movie has only strengthened my belief that we'll be getting our first glimpse of the new generation of Pokemon very soon. Should Gen 6 be revealed in the next few months, we will have to rethink everything we expect for the Pokemon series in SSB4, especially when it comes to the roster.