Mach Belt: I think they still say it's wearing a belt (so the question "where did the belt come from?" still remains), just the black "underwear" it has "on" is actually natural coloring.
Poke Attraction: As for the Gardevoir stuff, don't count GF out of the odd sexual obsession with it yet. Remember Mega Gardevoir does look like its wearing a wedding dress and it does form very close emotional bonds with its trainer... Oh, and GF also brought us not only a Pokemon who looks to be based off the Playboy bunny but Mega Lopunny's natural leg colors makes it look like its wearing torn stockings. Also not to mention that while they reused stock art of some of the male trainers from XY for ORAS all the female trainers got new art.
Gems: Careful there buddy, did you pull a muscle making that reference stretch? Want to try and throw in a Jem and the Holograms one as well while you're at it? :P
Anyway onto your questions:
1 & 2. As
Darth Manaphy pointed out, a few were causing havoc in the metagame, particularly Flying Gem + Acrobatics. You wouldn't think a one time 50% power boost would effect a battle that much, but I wouldn't be surprised if it was strong enough for a OHKO and that would affect a game a big way. Even with a 30% power decrease either tests they ran still showed it was too powerful (even if it didn't OHKO it would surely knock a Pokemon down to the low red range) or they didn't want to take the chance and pulled all of them (except for Normal Gem which we'll discuss below). I have a feeling they still want them in though, it's just they haven't had the time to figure out how (like give them out via Event Pokemon) or they're waiting for XY2/Z to give the metagame a chance to "reset and stabilize" before bringing them back for another test run. Thus why they also made the Fairy Gem, they want them to come back and they wouldn't feel complete with one for the new type (yet they didn't think to make a basic power-up item for Fairy-types...).
3. Outside of places like the Battle Subway and Pokemon World Tournament, not much if used at all. But that was probably due to their consumable nature. However in the Battle Subway and Pokemon World Tournament I imagine they were just as powerful as the were in the metagame. I think even some computer opponents us gems, many of the Gym Leader did (many using Flying Gem + Acrobatics and Dark Gem + Sucker Punch).
4. My guess Normal Gem was allowed since no Type is weak to Normal.
5. None that I can find.
I don't think Fairy Gem is a placeholder, if hacked it works as intended. And I don't see how not having a Fairy Gem would crash the game. Like Arceus had a ???-type (There was no ??? Plate though) to prevent crashing, but that's because someone may force Arceus to be a ???-type and since Arceus's sprite changes depending on its type the game would look for a ???-type Arceus sprite. Not so sure about the God Stone, that feels like its a leftover idea left in the game code. But its description is very simple and it does nothing.
Anyway, I hope they bring them back in XY2/Z. See if the changes you did work before tossing them out.