Well the theory is that Deoxys itself was created by the beam of the weapon, not that itself was involved in the creation of the weapon. It makes sense when you look at it's dex entries (which GF may have had in mind when making XY). GF tend to develop the remakes alongside the third versions (FrLg's close release date to Emerald's in Japanis a sign of that...I wonder if FrLg weren't released so close to Emerald than they might have done better, and GF mentioned how they developed Pt and HgSs simultaneously) too so they may be using OrAs as a steping stone for what's next. Actually the Mega Latis and Mega Blaziken seem to further hint that GF had in mind. I once read a rumor that GF think up what the next generation will be during the previous (for example Gen II during Gen I, Gen III during Gen II, and so on.)
Btw do you think they'll add some new story elements to MM, they did say they wanted to make it more than just a remake.
XY was only slightly bashed (at least from what I saw around the net) due to not being Hoenn remakes, most of the XY bashing was due to the plot and the lack of new Pokemon, evolutions of old mons, etc.
But yeah, that's true. Actually GF likely had ORAS itself planned out when they were making XY too (which may be hinted at by the Deoxys being connected to the Ultimate weapon (if the speculation of the Episode delta hinting at it is true)) which were in turned being developed some time around Gen V.
Considering that Anouma stated that MM3D was in development right after OoT3D was finished, it pretty much means all the fan demand were for nothing, because Nintendo does what Nintendo wants to do. It saddens me to see gamers wanting remakes of older games they've played before over new experiences like XY, which got bashed for not being Hoenn remakes, or Star Fox U and Spaltoon, which got people complaining about no Majora's Mask remake even though we've finally got a brand new Star Fox in years.
Because the internet is a powerful tool for riots, boycotts, and rebellions. Remember the Egyptian rebellion that happened a few years ago? It wouldn't have happened if not for the internet, which is why I fear the vocal minority will do the exact same thing to companies like Game Freak if they don't get what they want as perfect games.