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.
YMMV: Gunslinger Girl
Angst? What Angst?: Most cyborgs have their memories or their pre-Agency lives erased in order to remove the pain of past traumas (or make them easier to control, if you're cynical). Rico is unique in that she has full recollection of her time before she was given over to the Agency - which was not in itself a happy experience, with years crippled by birth defects and beset by quarreling parents - and is not at all troubled by years wasted in a hospital bed or being possessed by the Agency.
The ending credits music, Apres un Reve by Gabriel Fauré.
Ensemble Darkhorse: While Henrietta is ostensibly the focus character and the Henrietta-Guiseppe-Jean-MemoryOfEnrica plotline is the main narrative thrust of the work, fans at large have noticed over the years that the emotional impact, narrative depth, and generalized awesomeness of the series tends to get turned up to 11 any time Triela is involved in a scene or plotline.
Worth noting, Triela is the first of the girls we see "on the job".
Germans Love David Hasselhoff: In America, the first season was a modest success on DVD. In Japan, it was sold as a pack-in bonus for the licensed video game.
Harsher in Hindsight: The earlier deaths of Elsa and Lauro helped foreshadow the deaths of Henrietta and Jose.
Moral Event Horizon: Averted. When Pinocchio decides to kill Aurora for walking in on his affairs once too many (and given that he's falling in with some pretty shady people, he had every right to be concerned), Flanca orders him to not pull the trigger, thus preventing Pino from actually crossing the MEH.
Played straight by Ski Mask Guy in chapter 83, who crosses it just by showing up in front of Henrietta. The poor girl had lost her family to a couple of guys in ski masks, and just his appearance brought back those troubling memories and indirectly led to both her and Jose's deaths.
Dante was already established as a very bad man, but his personal MEH was orchestrating Sophie's death by car bomb, which also claimed everyone in the Croce family that wasn't named Jose or Jean.
Sequelitis: Despite being based on what is generally agreed to be the best part of the manga, Il Teatrino was poorly received in Japan and abroad for lesser animation quality, low or incorrect detail on the guns (in a series generally obsessive about firearms detail), inferior music to the original animation, and a complete swap-out of the entire vocal cast in Japan. It was also more action/thriller oriented than the first season, reflecting the manga, but considered to be to its detriment.
Values Dissonance: Any Italian would find all of the relationships unspeakably cold and distant since the author, in a classic case of cultural projection, has depicted the characters with Japanese reserve instead of Italian brio — even to the extent of them bowing on occasion.
This becomes a bit of Fridge Brilliance for the relationships between the girls and the handlers/staff because it represents just how uncomfortable everyone is around these walking killing machines. And the distance between Giuseppe and Jean is part of the point, though many of the more background characters are straight examples.
The Woobie: As a consequence of being an Ill Girl, Angelica excites a great deal of sympathy from many readers - to the extent that many were actually dissatisfied with her appearance in Il Teatrino. Although Angelica was alive at the equivalent point in the manga, the first series of the anime ended with her implied death and many considered her reintroduction to have spoiled a beautiful tragedy.