They Wasted a Perfectly Good Plot/Character: Think of the story potential if Precia had been a loving mother to Fate, despite grieving over Alicia and realizing Fate is different. Her demise would have had much more impact that way. Fate would have been forced to defeat her beloved mother in order to save millions of lives. Better still, Fate could even have been longing herself for Alicia's resurrection, so she could finally meet her "sister". Alas, the makers obviously wished for Precia to be a card carrying villain, so Fate could be presented as an innocent victim.
The Woobie: Fate. She just wants please her mother, but nothing she does over the course is ever good enough for her and she gets horribly abused no matter what she does. Towards the end of the series, even she finds that she was just an Artificial Human modeled after Precia's real daughter Alecia, and that Precia never thought of her as her daughter, she still tries to make amends with her.
Jerkass Woobie: Precia in contrast to the original incarnation. She's still a cruel bitch of course, but you can feel bad for her too, especially since you often do see her expressing emotions besides her typical cold disdain and occasional insane glee, like when she finds Alicia's lifeless body. She's even implied to regret what she did at the end. Since it is an in-universe biographical movie, the inconsistency is explained with Fate insisting on a more sympathetic portrayal of her.
Pandering to the Base: While Fate got a transformation, Nanoha's transformation was more fanservice-based and Bardiche and Raising Heart both got new looks, but there's a lot of information that ONLY fans of the series would know that didn't make it in the movie.
Nanoha is considerably more angsty in the movie manga, and some people believe she falls into this at times. For example, while at the end of the Jewel Seed case in the original anime, she was mostly satisfied with how things turned out but somewhat worried about Fate, she believes in the movie manga that she was unable to help anyone at all. This has lead to the Fan Nickname "Emoha" for this version of Nanoha.
In fact, the manga's story is quite a bit more gratuitously angsty in general. Fate doesn't recover from her Heroic BSOD in time to either team up with Nanoha or confront Precia, Chrono blames himself for the trauma that Nanoha and Fate went through, the general consensus among the Arthra's crew is that the jewel seed incident was a lost cause, and even freaking Raising Heart angsts when it thinks that it's given Nanoha faulty combat advice.
The Woobie: Linith. Her plight is even more poignant in the movie manga, as she reveals that she wanted to take Fate and Arf away from Precia, but knew that doing so would hurt her, and realized that Precia and by extension, herself as Precia’s familiar had no more than two years to live. She thus did her best to ensure that Fate became strong and had a good relationship with Precia, and told Fate that she hoped she would find a good friend.