These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Americans Love Mana Khemia: In Japan, the two Mana Khemia games received a fairly lukewarm reception from the established fanbase, and Mana Khemia 2 received a lot of flak from reviewers. In the West, on the other hand... well, just take a gander at which of the dedicated game pages is longest and which one received so much attention as to warrant its own character page (and reportedly sold better in the West than it did in Japan). MK 2 also got a much warmer reception from the Western press than it did in Japan, scoring slightly higher on average than MK 1 did. (This may have something to do with those Game Breaking Bugs getting fixed for us, though.)
Broken Base: In some ways, the Arland games are causing this. Certain fandom sections, like those found at Sankaku Complex, basically describe the Arland games (and thus the wider franchise) as "eroge without the actual ero bits" and are mostly in it for the girls and, uh, what they can dowith them. This makes many older Atelier fans bristle with rage, as the games have never been intended to be erotic; Marie's odd chest... thing aside, the hottest any pre-Iris game got was having Lilie in a nightgown for one scene. note And really, the hottest any post-Iris game got was a chest-and-up Barbie Doll Anatomy scene of Lita in a tank in Iris 1. The actual Arland games don't help at all, either; on the one hand, there's the occasional scene with, uh, what can only be called "overtones"◊ (possibly nsfw), but on the other hand many scenes seem dedicated to making fun of this kind of nonsense in the same way Ar tonelico does. At this point many people aren't quite sure what to think, but the debate rages on.
Crowning Music of Awesome: Gust Sound Team is only slightly less well-known than Falcom's JDK Band in this regard in Japan. For organizational purposes, their work gets lumped in with NIS stuff on TVT, but good lord, this series has had a lot of good music, especially from the second game on. The Iris games in particular produced some amazing vocal and boss themes, and Atelier Violet is basically one huge crowner for the entire team.
Ensemble Darkhorse: In a franchise as big as this one, you'd expect this to happen a few times, and it certainly has.
The one most Americans will be familiar with is Veola from Atelier Iris 1; there are suspicions that said game might have started life as "Atelier Veola" and then gotten development shifted partway through into what it is now. The result, though, is that this one shopkeeper, who doesn't seem all that important initially, has as much story content tied to her as the main plot, and many find it more engaging than the actual plot of AI 1. A lot of people don't play the game for Klein or Lita, they play it for Veola, and she's far and away the most popular character both in Japan and overseas.
As popular as Veola is, though, the absolute queen of Atelier Darkhorses is, without a doubt, Helmina of the original series. Introduced as a kind of pseudo-villain in Atelier Elie, she was so well-written, so engaging, so interesting and so casually evil (she even comes close to killing Elie with a narcotic potion that could stop her heart, and she applies the antidote just in time for Elie to not die; she does this out of curiosity) that the Japanese fanbase fell in love with her immediately. Her portrayal in supplementary materials, such as various spinoff manga, only cemented her popularity further. She became so popular that she (and Ingrid, from Atelier Marie) were put into Atelier Lilie as the Kid Sidekicks to the heroine of that game, and the popularity of the more innocent Helmina portrayed here compelled Gust to release Helmina & Culus, a product that is essentially an expansion to Lilie and finally features Helmina in a starring role (and portrays what would become Helmina's Start of Darkness).
She then shows up as a wandering alchemist party member in Atelier Judie, which still takes place some time before she becomes a teacher in Atelier Elie. This would be her last appearance, however, as after Atelier Violet Gust began to create continuities separate from the original "Salburg" one. Helmina still holds the record for consecutive product appearances, however, all due to fan demand.
Flay Gunnar (AKA "Gunnar Damm") of Mana Khemia certainly qualifies as well. People identified with him quite a bit more than with the main heroes of the first game, and the response to him in both Japan and America was so overwhelmingly positive that he got a spot in Mana Khemia 2 almost by force.
Game Breaker: Since in some of the games you can craft your own weapons and armor or items with certain properties, knowing the right combination of ingredients and synthesis steps will allow you to craft equipment and items that just do absurd things. Like how about having a healing item that restores all HP, MP, status, and does it again f after everyone else has had a turn?
Seinfeld Is Unfunny (AKA, Alchemy Is Unoriginal): Quite a few prospective fans and consumers have pooh-poohed the games that have crossed over for being unoriginal in story and for crafting and alchemy being "nothing really special". While the story criticisms for the Iris games are probably not unwarranted, the early games were the games which introduced robust crafting systems into JRPGs in the first place and were also the first ones to use alchemy as a world-framing concept in Japanese pop culture. Thanks to the sluggishness of the series in crossing the Pacific, however, everything influenced by the series got here first and made Atelier look like the unoriginal one.
Sequelitis: Even the most die-hard Gust fanboy has to admit that, with no less than one release every year, the franchise has ached at times due to all of its sequels; even attempts to legitimately mix up the franchise such as Mana Khemia or Atelier Annie (which added a little Simulation Game to the mix, with its focus on helping to develop an island) sometimes came off as a bit stale, and quality assurance took a precipitous dip in the late Noughts, as evidenced by Atelier Liese and Mana Khemia 2 and their evisceration in the Japanese gaming press (to say nothing of Liese's terrifyingly massive published bug list and gamecard-swap program). The series is currently on a roll again, but there are fears it could burn out again if not given a chance to rest.
Squick: Due to the nature of the alchemy system in some games (especially the Arland set), it's possible to put some very strange things into your food items. Rorona is capable of turning nearly anything into a pie... including stuff like fertilizer. Ayesha can put actual cow droppings into some of her stuff, too.
Surprisingly Improved Sequel: Given how long the series has run it can be expected that the series has had some ups and downs, but there have been a few real leaps in quality.
The first was between the first two games, Marie and Elie. Marie was a very simple game produced on a tiny budget, and it showed in how relatively simple and light the content was. Elie was produced after the money from Marie rolled in, and not only features a ton of engine improvements but features approximately three to four times the story content of the previous game, making it, until recently, the fan favorite of the series in Japan.
Another was Judie to Violet: Judie was a fairly disappointing game that took away some of the elements of previous games in an apparent attempt to broaden franchise appeal (and failed badly); Violet took the few good things from Judie, wedded them to the systems of the older games, and is generally seen as being in a dead heat for "Best PS2 Atelier Game" alongside Mana Khemia.
Liese to Annie. Liese was infamously buggy, had a somewhat annoying combat system and didn't really have enough story content, leading to it getting ripped to shreds in Japan. Annie, on the other hand, not only launched bug-free but addressed every single gameplay issue in Liese and features a lot more story content, to the point where it's even receiving positive press in the West.
Finally, some are claiming that the Arland series, Atelier Meruru in particular, is this to most of the franchise. As PS3 games which went nearly full-on 3D while still bringing the old alchemy-centric gameplay back to consoles after half a decade out in the cold, a lot of gamers on both sides of the Pacific took a shine to what the games did. The fact that the Arland games were first time since the PS1 era that the franchise sold six-figures consistently is not hurting this perception.
Surprise Difficulty: If you look at the art of Atelier Annie, it's a little bit cute compared to the Iris games. There's more than a few bishounen characters in the cast. And the cover has an E10+ rating. But this is also a game where if the player rushes into battle without bringing healing items or changing the heroine's equipment, then a single Puni can kill her.
Most of the early Ateliers were like this; if you were too lax in recruiting some party members, didn't upgrade equipment or went too far from town too quickly, you could quickly find yourself overwhelmed. This is part of what made Atelier LilieNintendo Hard, since your starting party options consist of your twentysomething alchemist heroine and her two ten-year-old hangers-on. They can easily go out into the woods and get mauled to death by wolves at the start of the game.
Tear Jerker: Friggin' everything in Helmina & Culus. It chronicles how Helmina became friends with the first homunculus she ever made, and how it's doomed to live a short life, and how this traumatic experience turns her into the bitter, jaded, sarcastic, and frankly evil woman we see in Atelier Elie and Atelier Judie. And then they do all sorts of cute things together, oh god. How could it not have content that constantly rips at your heartstrings?
The earlier "free-form alchemy" games, as well as their most recent successors, can hit you with this out of nowhere, too, given their non-linear nature. A good example is Gillian in Atelier Annie; for most of the game she's a lazy, happy-go-lucky Lethal Chef who is easy to get along with... and then you find out just why she's so obsessed with herbal health drinks.
That One Boss: Beginning with Prism, almost everyone in the latter half of Atelier Iris: Eternal Mana and the Slaith Reincarnation in Atelier Iris 2. Averted in the third Iris game wher Shadow Stalker, the One Boss, is completely optional (although you'll miss out on the Luplus Blades.)
Unfortunate Implications: The games do occasionally tread on this ground. The desert natives in Iris 2 look and act just like Native Americans, which might be unfortunate depending on your point of view... and in the early games, you can hire "fairies" to help you around your atelier with item creation, resource gathering, etc. Except the black-colored ones are the cheapest, least efficient, and laziest. Oh dear...
This is made even more disappointing in that, by and large, the series contains some of the most progressive depictions of female lead characters in the history of the medium. Even then they're, uh, all Caucasian, however.
Justified (kind of, anyway) in that there wasn't exactly a lot of skin color variation in Renaissance Germany, on which the setting of the early games is based.
Woolseyism: There have been a few in the games that have crossed the sea so far; the aforementioned ESRB Joke is practically the Clinton Joke of the Noughties at this point.
Gillian Clout of Atelier Annie is another good one; her name was initially given in Japanese sources as "Jalia Kraut". Thankfully NISA had the good sense to put that to bed quick-smart.