The crystals. If you're on a 1.4.7 pack, just make yourself a quick x-ray system (TNT/glowstone through the head) and you'll see why. There's also how they damage everything they touch, so tough luck if you mined a diamond that just happened to be right above one of them!
You could just as easily have lost it to lava, but it's not exactly hard to stand close enough to pick it up before they get destroyed.
As far as I'm concerned losing materials while mining is not a prolific problem because it can be easily avoided so xycraft has added no new dangers.
As for the amount of materials found in world gen, i do think Xycraft has gone overboard, I've only ever had a shortage of anything from xycraft so i think it would add value to the mod to add some rarity.
But to address community demands for quality etc. you should read up on Xycraft because the only reason its out right now is because the community demanded it was released and the developer trying to convince people it wasn't ready not the other way around.
In my opinion Xycraft is not in anyway a bad mod, it just isn't finished yet.
So should it be in the mod packs yet?, i don't know but i certainly enjoy playing with it and would add it personally myself.