BW and BW2 were compatible, right? What happened when somebody used Kyurem-Black in battle against BW players. The fact that Sceptile can't Mega Evolve in XY is no different than Kyurem not fusing in BW.
No, it is completely different. The exact same thing happened in Gen IV with Shaymin and Giratina.
Introducing new forms like that worked because it doesn't happen in battle. As far as DP knew, the Giratina just had a weird ability and weird stats. Shaymin was the same way (although it also had a weird type). Same for Kyurem.
Mega Evolution however occurs mid-battle. There's just no way to get around it by trying to "hide" the Mega Evolution.
Game Freak has patched the game for a game-breaking save glitch; even if it's not an easy process they've done it for more important reasons than including new Megas, and I doubt they had planned something like that (I would honestly hope not, at least).
Exactly. They had no way of getting around patching. They had to. This is different from intentionally planning on patching just to add something as simple as connecting to ORAS, which, since it is going to be important for many people, should just be in from the get-go.
As for the events, you basically answered your own question: why go through the trouble? Those events, excepting maybe the Eon Pokémon, are Kalos Pokémon, and likely Kalos events. For them, its easier--and makes sense--for them to be in the games from the get-go.
How did I answer my own question? My point was that the hidden Pokemon were just that.
Hidden. The fact that they are Kalos Pokemon doesn't change the fact that they wanted them to be hidden - not known by the general public. How would it make sense for them to care more about keeping, say, a Mega Sceptile secret than something like Hoopa?
If they honestly believe they have a good distribution method for a patch for ORAS compatibility (which would have to distributed to essentially everyone), and since they wanted to keep them secret, there is
no reason to not create a patch for them as well.
Would it be more effort than leaving it in from the beginning? Yes, of course. But then, so would intentionally leaving out Megas to include in ORAS.