Atelier Annie is part of a real grey area in desirability called the NIS Store LE problem. They pump out a metric ton of LEs for just about every game they release, a lot of them nothing more than a bonus box they ship with the game. While that's all well and good, every collector knows about them and if they want them, they get them. 550 is a low print run for sure, but if everyone who wants it, gets it (and moreso gets it JUST because they think it's going to be pricey/hard to find later)... there will be no demand and no value and no desirability.
The other games you mentioned could surely be desired titles, but I don't think they'll ever fetch more than what they originally sold for, at least for a good while.